http://genome.sph.umich.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Shuang+Feng Genome Analysis Wiki - User contributions [en] 2026-10-13T05:37:00Z User contributions MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=Abecasis_Lab&diff=14536 Abecasis Lab 2017-01-10T03:44:17Z <p>Shuang Feng: /* Former Doctoral Students */</p> <hr /> <div>[[Image:AbecasisRetreat2016.jpg|700px|center|Group Photo 2016]]<br /> <br /> <br /> &lt;!--[[Image:Abecasis2015Retreat.JPG|400px|center|Group Photo]]--&gt;<br /> <br /> == Mission Statement ==<br /> <br /> We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.<br /> <br /> == Leadership ==<br /> <br /> [[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.<br /> <br /> == Current Members ==<br /> <br /> === Research Fellows ===<br /> <br /> [[File:Kuser.png|50px]] Christian Fuchsberger<br /> <br /> [[File:Sarah.jpg.jpg|50px]] Sarah Gagliano<br /> <br /> [[File:PicJingjing.jpg|50px]] Jingjing Yang<br /> <br /> === Graduate Students ===<br /> <br /> <br /> [[File:SaiChen.jpg|50px]] Sai Chen<br /> <br /> [[File:Kuser.png|50px]] Priscilla Geng<br /> <br /> [[File:HeadOfAlanKwong.jpg|50px]] [[Alan Kwong]]<br /> <br /> [[File:Kuser.png|50px]] Sebanti Sengupta<br /> <br /> [[File:Kuser.png|50px]] Joshua Weinstock<br /> <br /> [[File:Gregory3.jpg|50px]] Greg Zajac<br /> <br /> [[File:Kuser.png|50px]] Fan Zhang<br /> <br /> [[File:Kuser.png|50px]] Wei Zhou<br /> <br /> [[File:Xutong.jpg|50px]] Xutong Zhao<br /> <br /> === Staff ===<br /> <br /> [[File:Irene_headshot.jpg|50px]] Irene Felicetti : Administrative Assistant Sr. <br /> <br /> <br /> [[File:TomBlackwell_crop.jpg|50px]] [[Tom Blackwell]] : Research Area Specialist Sr. <br /> <br /> [[File:Sean_head.jpg|50px]] [[Sean Caron]] : UNIX Systems Administrator<br /> <br /> [[File:Headshot-chris-clark-2 (3).jpg|50px]] Chris Clark : Applications Programmer/Analyst Sr.<br /> <br /> [[File:Kuser.png|50px]] Jonathon LeFaive : Applications Programmer/Analyst Sr.<br /> <br /> [[File:Kevin_Web-Profile.jpg ‎|50px]] Kevin Li : Web Applications Developer<br /> <br /> [[File:IMG_4735.JPG|50px]] Anita Pandit : Research Computer Specialist<br /> <br /> [[File:Schmidt_small.jpg|50px]] Ellen Schmidt : Research Area Specialist Lead<br /> <br /> [[File:pjvh.jpg|50px]] Peter VandeHaar : Applications Programmer/Analyst Sr.<br /> <br /> [[File:MK_head.jpg|50px]] [[Mary Kate Wing]] : Applications Programmer working on GotCloud Pipelines, C++ library &amp; tools (libStatGen, bamUtils)<br /> <br /> == Alumni ==<br /> <br /> === Former Research Faculty ===<br /> <br /> * Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].<br /> <br /> === Former Research Fellows ===<br /> <br /> * Weimin Chen (graduated 2007), now Associate Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences &amp; Center for Public Health Genomics, University of Virginia]<br /> <br /> * Goo Jun (graduated 2008), now Assistant Professor at the [https://scholar.google.com/citations?user=1wzhcEQAAAAJ&amp;hl=en University of Texas Health Sciences Center]<br /> <br /> * Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]<br /> <br /> * [[Dajiang Liu]] (graduated 2013), now Assistant Professor at the [http://www-personal.umich.edu/~dajiang/ Penn State University College of Medicine]<br /> <br /> * Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]<br /> <br /> * Paul Scheet (graduated 2008), now Associate Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]<br /> <br /> * Carlo Sidore (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]<br /> <br /> * Fabio Busonero (graduated 2012), now an investigator at the [http://www.cnr.it/istituti/DatiGenerali.html?cds=060 Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]<br /> <br /> * William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]<br /> <br /> * Alex Tsoi (graduated 2014), now Research Assistant Professor at [https://www.med.umich.edu/DERM/faculty/alextsoi_pub.shtml University of Michigan Medical School]<br /> <br /> * [[Scott Vrieze]] (graduated 2014), now an Assistant Professor of Psychology and Neuroscience at [http://www.colorado.edu/ibg/people/471 University of Colorado, Boulder]<br /> <br /> * [[Lars Fritsche]] (graduated 2016), now an Associate Professor at [http://www.ntnu.edu/ism the Department of Public Health and General Practice at the Norwegian University of Science and Technology] in Trondheim, Norway<br /> <br /> === Former Doctoral Students ===<br /> <br /> * Katharine Brieger, now Graduate Student, Epidemiology, School of Public Health, University of Michigan<br /> <br /> * Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]<br /> <br /> * Jun Ding (graduated 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].<br /> <br /> * Shuang Feng (graduated 2015), now Senior Data Scientist at Uber.<br /> <br /> * Weihua Guan (graduated 2010), now Assistant Professor at the [http://sph.umn.edu/faculty1/expertise/statistical-genetics/name/weihua-guan/ Department of Biostatistics, University of Minnesota School of Public Health].<br /> <br /> * Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&amp;Itemid=6138&amp;profileAction=ProfDetail&amp;pid=708777879 Department of Biostatistics, University of North Carolina].<br /> <br /> * Youna Hu (graduated 2012), now a Data Sciences Engineer at A9, a subsidiary of 23andMe, Inc.<br /> <br /> * Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]<br /> <br /> * Liming Liang (graduated 2009), now Associate Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]<br /> <br /> * Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]<br /> <br /> * Sara Rashkin (graduated 2015), now Post Doc at [http://wittelab.ucsf.edu/pages/people UCSF Witte Lab]<br /> <br /> * Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]<br /> <br /> * [[Xiaowei Zhan]] (graduated 2014), now Assistant Professor at the [http://profiles.utsouthwestern.edu/profile/152189/xiaowei-zhan.html Department of Clinical Science, University of Texas - Southwestern Medical Center].<br /> <br /> * Jin Zheng (graduated 2009), now working in the Pharmaceutical Industry at Eli Lilly.<br /> <br /> === Former Masters Students ===<br /> <br /> * Su Chu<br /> <br /> * Nate Cohen<br /> <br /> * Melinda Curran<br /> <br /> * Vesela Gateva<br /> <br /> * Xijing Han<br /> <br /> * Dan Hovelson<br /> <br /> * Elizabeth Jewell<br /> <br /> * Michelle Kleckner<br /> <br /> * Ben Lerch<br /> <br /> * Yanming Li<br /> <br /> * Heather Munro<br /> <br /> * Nick Seewald<br /> <br /> * Theresa Scott (nee Daigneault)<br /> <br /> * Matthew Snyder<br /> <br /> * Vivian Wang<br /> <br /> * Yuan Wei<br /> <br /> * Abigail Woodroffe<br /> <br /> * Zaojun Ye<br /> <br /> * Matthew Zawitowski<br /> <br /> * Anita Yu Zhao<br /> <br /> * Wanlin Zheng<br /> <br /> * Tingting Zhou<br /> <br /> === Former Staff ===<br /> <br /> * Paul Anderson<br /> <br /> * Laura Baker<br /> <br /> * [[Jennifer Bragg-Gresham]]<br /> <br /> * Johanna Forster<br /> <br /> * Jan Wigginton<br /> <br /> === Visitors ===<br /> <br /> * Qing Lu<br /> <br /> * Andrea Maschio<br /> <br /> * Giorgio Pistis<br /> <br /> * Eleanora Porcu<br /> <br /> * Toshiko Tanakato<br /> <br /> == Really Useful Stuff ==<br /> <br /> * [[Abecasis Group Awards]]<br /> * [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:LINUX_raremetal.4.13.6.tgz&diff=12984 File:LINUX raremetal.4.13.6.tgz 2015-03-09T07:41:06Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:MAC_raremetal.4.13.6.tgz&diff=12983 File:MAC raremetal.4.13.6.tgz 2015-03-09T07:37:07Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:CYGWIN64_raremetal.4.13.6.tgz&diff=12982 File:CYGWIN64 raremetal.4.13.6.tgz 2015-03-09T07:36:03Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:MINGW_raremetal.4.13.6.tgz&diff=12981 File:MINGW raremetal.4.13.6.tgz 2015-03-09T07:34:41Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12980 RAREMETAL DOWNLOAD & BUILD 2015-03-09T07:33:28Z <p>Shuang Feng: /* EXECUTABLES */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.6, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.6.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.6.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.6.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.6.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.linux.executable.4.13.6.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.6 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:Raremetal.linux.executable.4.13.6.tgz&diff=12979 File:Raremetal.linux.executable.4.13.6.tgz 2015-03-09T07:32:57Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12978 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:28:27Z <p>Shuang Feng: /* EXECUTABLES */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.6, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.6.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.6.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.6.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.6.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.6.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.6 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12977 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:28:02Z <p>Shuang Feng: /* SOURCE CODE */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.6, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.6.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.6.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.6.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.6.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.5.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.6 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12976 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:27:41Z <p>Shuang Feng: /* RAREMETAL 4.9 and after */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.5, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.5.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.5.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.5.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.5.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.5.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.6 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12975 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:27:26Z <p>Shuang Feng: /* Calculating Odds Ratio from RAREMETALWORKER output */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.5, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.5.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.5.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.5.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.5.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.5.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.5 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12974 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:27:14Z <p>Shuang Feng: /* How to Compile */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.5, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.5.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.5.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.5.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.5.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.5.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.5 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.6.tgz<br /> prompt&gt; cd raremetal_4.13.6<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.5 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETAL_DOWNLOAD_%26_BUILD&diff=12973 RAREMETAL DOWNLOAD & BUILD 2015-03-09T06:26:53Z <p>Shuang Feng: /* RAREMETAL 4.9 and after */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]<br /> * The [[RAREMETAL FAQ | '''FAQ''']]<br /> <br /> == Where to Download ==<br /> <br /> ===SOURCE CODE===<br /> <br /> We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RHEL, Linux/CentOS, Mac OS X 10.8, CygWin64 and MinGW for Windows.<br /> From version 4.13.5, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. To download source code for each platform, please go to the following:<br /> <br /> * [[Media:LINUX_raremetal.4.13.5.tgz ‎|'''for Linux''']] <br /> <br /> * [[Media:MAC_raremetal.4.13.5.tgz ‎|'''for MAC OS X''']]<br /> <br /> * [[Media:CYGWIN64_raremetal.4.13.5.tgz ‎|'''for Windows/CygWin64''']]<br /> <br /> * [[Media:MINGW_raremetal.4.13.5.tgz ‎|'''for Windows/MinGW''']]<br /> <br /> ===EXECUTABLES===<br /> <br /> Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.<br /> *[[Media:Raremetal.4.13.5.linux.executable.tgz|'''for Linux''']]<br /> <br /> ===SCRIPTS===<br /> <br /> ====Calculating Odds Ratio from RAREMETALWORKER output====<br /> *If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column. <br /> *The script can also be found in the RAREMETAL package 4.13.5 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.<br /> <br /> == How to Compile ==<br /> <br /> * gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.<br /> <br /> * If you choose to build from the source files, you could start from decompress the package using the following command:<br /> prompt&gt; tar xvf LINUX_raremetal.4.13.5.tgz<br /> prompt&gt; cd raremetal_4.13.5<br /> <br /> * If you prefer to build two tools all at once, then do the following:<br /> prompt&gt; cd raremetal<br /> prompt&gt; make<br /> #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. <br /> <br /> * If you prefer to build individual tool:<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> prompt&gt; cd raremetal/raremetal/src<br /> prompt&gt; make<br /> #This will build RAREMETAL under raremetal/bin/ directory.<br /> <br /> * If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to [http://openmp.org/wp/openmp-compilers/ openMP].<br /> prompt&gt; cd raremetal/raremetalworker/src<br /> prompt&gt; make openmp<br /> #This will build RAREMETALWORKER under raremetal/bin/ directory.<br /> <br /> * If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.<br /> <br /> ==FAQ==<br /> <br /> For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.<br /> <br /> ==Change Log==<br /> <br /> ===RAREMETALWORKR 4.8 and before===<br /> * Version 0.0.1 was released on 11/13/2012.<br /> * Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)<br /> * Uploaded to public wiki. (11/16/2012)<br /> * Enabled writing log file by defalut. (11/18/2012)<br /> * Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)<br /> * Added HWE pvalue and call rate in summary statistics output. (11/27/2012)<br /> * Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)<br /> * Updated output format. Version 0.0.3 released. (12/3/2012)<br /> * More messages coded into log file. (12/4/2012)<br /> * Version 0.0.4 released. (12/5/2012)<br /> * Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)<br /> * Version 0.0.6 released. (12/6/2012)<br /> * Updated output format for monomorphic sites. (12/7/2012)<br /> * Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)<br /> * Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)<br /> * Fixed a bug when there is missing genotype from VCF file. (2/2013)<br /> * Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)<br /> * Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)<br /> * Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)<br /> * Fixed bug in handling chromosome X. Added sanity checking steps before analysis. Added graphic support by generating QQ and manhattan plots automatically. Upgraded tool to version 2.8. (till 8/12/2013)<br /> * Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)<br /> * Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)<br /> * Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)<br /> * Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)<br /> * Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)<br /> * Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.<br /> * Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.<br /> * Released version 0.4.2. Fixed a bug that could possibly cause compiling error in some Linux system. Also, in this version, male heterozygous genotypes on chromosome X are considered missing. (3/10/2014)<br /> * Released version 0.4.3. Fixed a few typo in messages. Added --noeof option for VCF files that does not have a BGZF EOF marker.<br /> * Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)<br /> * Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)<br /> * Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)<br /> * Released version 0.4.7 binary and source code. Optimized code to increase analysis efficiency and reduce memory use. Added --separateX option to provide another choice of analyzing chromosome X. Added --kinxFile option to allow kinship X matrix file with different prefix from the autosomal kinship.(4/2/2014)<br /> <br /> ===RAREMETAL 4.8 and before===<br /> * Version 0.0.1 released to U of M CSG group. (2/13/2013)<br /> * Version 0.0.1 released. (2/24/2013)<br /> * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)<br /> * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)<br /> * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.<br /> * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.<br /> * Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.<br /> * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)<br /> * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)<br /> <br /> ===RAREMETAL 4.9 and after===<br /> * version 4.10: fixed a bug when analyzing multiple traits is requested in raremetalworker (bug only in version 4.9 and later, and doesn't affect results).<br /> * version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).<br /> * version 4.12: improved make file for better compilation.<br /> * version 4.12.1: fixed command interface display issue in raremetalworker.<br /> * version 4.13: fixed bug when using --vcX option. Fixed bug estimating kinshipX with female samples. Added --kinOnly option for generating kinship only without association analysis. Added --geneMap option to allow user input for gene-mapping file.<br /> * Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.<br /> * Version 4.13.2 fixed sqrt_V output when analyzing unrelated individuals without kinship and --inverseNormal is not used and trait variance is not one.<br /> * Version 4.13.3 released to read rvtest output format correctly in raremetal.<br /> * Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.<br /> * Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)<br /> * Version 4.13.5 released with a new option --mergedVCFID to recognize VCF files with sample IDs in &quot;FAMID_PID&quot; format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETALWORKER_command_reference&diff=12972 RAREMETALWORKER command reference 2015-03-09T06:17:00Z <p>Shuang Feng: /* --geneMap */</p> <hr /> <div>==Useful Links==<br /> <br /> Here are some useful links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]<br /> * The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]<br /> * The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']]<br /> * The [[RAREMETAL_FAQ | '''FAQ''']]<br /> <br /> Options:<br /> Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],<br /> --noeof<br /> Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,<br /> --labelHits<br /> VC Options : --vcX, --separateX<br /> Trait Options : --makeResiduals, --inverseNormal, --traitName []<br /> Model Options : --recessive, --dominant<br /> Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],<br /> --kinSave<br /> Kinship Options : --kinMaf [0.05], --kinMiss [0.05]<br /> Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],<br /> --maleLabel [1], --femaleLabel [2]<br /> others : --cpu [1], --kinOnly,<br /> --geneMap [../data/refFlat_hg19.txt], --mergedVCFID<br /> PhoneHome : --noPhoneHome, --phoneHomeThinning [100]<br /> <br /> ==Input Files==<br /> ===--ped===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format PED''']] file name.<br /> ===--dat===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format DAT''']] file name.<br /> ===--vcf===<br /> *--vcf takes a string of your [[RAREMETALWORKER#VCF_File | '''VCF''']] file name.<br /> ===--dosage===<br /> * When --dosage is issued in command line, RAREMETALWORKER reads dosage from your [[RAREMETALWORKER#VCF_File | '''VCF''']] file.<br /> * --dosage must be used with --vcf option.<br /> * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']].<br /> <br /> ===--flagDosage===<br /> * This option let user customize the name of field in VCF file that labels dosage data.<br /> * The default is &quot;DS&quot;.<br /> <br /> ===--noeof===<br /> * If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file. <br /> * Please see [[RAREMETAL_FAQ#error:_BGZF_EOF_marker_is_missing_in_xxx.vcf.gz | '''BGZF EOF''']] for more details.<br /> <br /> ==Output Files==<br /> <br /> ===--prefix===<br /> * --prefix takes a value of a string as the prefix of your output files. <br /> * For a full list of output files generated by RAREMETALWORKER, please refer to [[RAREMETALWORKER#OUTPUT_FILE_FORMATS | '''output''']].<br /> <br /> ===--LDwindow===<br /> *--LDwindow takes a integer value as the size of the moving window. <br /> * RAREMETALWORKER generates LD matrices between a current marker that it is working on and all markers within this window.<br /> * The default size is 1 million bases.<br /> * For more information about the LD matrix, please refer to [[RAREMETALWORKER#LD_Matrices | '''LD matrix''']].<br /> <br /> ===--zip===<br /> * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. <br /> <br /> === --thin ===<br /> * If --thin is issued, then RAREMETALWORKER generates [[RAREMETALWORKER#Plots | '''QQ plots and Manhattan plots''']] with less resolution (points), to make the pdf files smaller in size.<br /> <br /> ===--labelHits===<br /> * If --thin is issued, then RAREMETALWORKER automatically label the loci that are above a threshold.<br /> * The threshold is calculated using Bonferroni correction (''0.05/N, where N is the total number of polymorphic markers'').<br /> <br /> ==VC Options==<br /> <br /> ===--vcX===<br /> * --vcX option has to be used with --kinPedigree (when pedigree kinship is used), or --kinGeno (when genomic relationship matrix is estimated), or --kinFile ( when GRM is read from a file). <br /> * Using --vcX option let RAREMETALWORKER fit a linear mixed model to analyze chromosome X, using both autosomal kinship and chromosome X kinship. <br /> <br /> ===--separateX===<br /> * --separateX option must be used with --vcX option. <br /> * Using --separateX option requests RAREMETALWORKER to fit a linear mixed model using only chromosome X kinship for analyses of chromosome X markers. <br /> <br /> Please refer to [[RAREMETALWORKER_method#ANALYZING_MARKERS_ON_CHROMOSOME_X| '''method''']] and [[RAREMETALWORKER_SPECIAL_TOPICS#Analyzing_Chromosome_X | '''technical details''']] for more explanation.<br /> <br /> ==Trait Options==<br /> ===--makeResiduals===<br /> * If --makeResiduals is used, then covariates are adjusted before fitting linear models using residuals.<br /> <br /> ===--inverseNormal===<br /> * If --inverseNormal is used, but not with --makeResiduals, then trait values are inverse normalized before fitting linear models.<br /> * If --inverseNormal and --makeResiduals are used together, then covariates are adjusted and inverse normalized residuals are used to fit linear models. <br /> <br /> ===--traitName===<br /> * --traitName takes a string of the trait name that you want to analyze. <br /> * If this option is not used, then all traits included in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED/DAT''']] files are analyzed.<br /> <br /> ==Model Options==<br /> ===--recessive===<br /> * If --recessive is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''recessive output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.recessive.plots.pdf''.<br /> ===--dominant===<br /> * If --dominant is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''dominant output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.dominant.plots.pdf''.<br /> <br /> ==Kinship Source==<br /> ===--kinPedigree===<br /> * If --kinPedigree is used, pedigree structure coded in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file is used to generate a kinship matrix for later fitting linear mixed model before associations. <br /> <br /> ===--kinGeno===<br /> * If --kinPedigree is used, then a genomic relationship matrix is estimated from genotype. <br /> * If --vcX option is used, then a separate genomic relationship matrix for chromosome X is also estimated. <br /> * For details about how to estimate GRM, please refer to [[RAREMETALWORKER_method#MODELING_RELATEDNESS | ''methods''']].<br /> <br /> ===--kinFile===<br /> * --kinFile takes a string of the file name of previously saved GRM with format described in [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> * This option reads GRM from the file and then extract the correct GRM based on samples to be analyzed according to your specifications, such as traits to be analyzed, missing covariates and genotypes (please refer to [[RAREMETALWORKER_SPECIAL_TOPICS#Missing_Data | '''missing data''']] for more details).<br /> * --kinFile can not be used together with --kinGeno. <br /> <br /> ===--kinxFile===<br /> * --kinxFile must be used with --kinFile and --vcX. <br /> * --kinxFile takes a string of file name of the previously saved GRM for chromosome X. <br /> * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur.<br /> ===--kinSave===<br /> * This option must be used with --kinGeno.<br /> * Issuing --kinSave will request [[RAREMETALWORKER]] to store the estimated GMR in a file named yourprefix.Empirical.Kinship.gz.<br /> * If --vcX is also issued in the command line, then a separate file named yourprefix.Empirical.KinshipX.gz will be generated where the GRM of chromosome X is saved.<br /> *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> <br /> ==Kinship Options==<br /> ===--kinMaf=== <br /> * --kinMaf takes a value that specifies the MAF cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with MAF&lt;0.05 are not used for estimating GRMs.<br /> ===--kinMiss===<br /> * --kinMiss takes a value that specifies the missing genotype cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with genotype call rate &lt;0.95 are not used for estimating GRMs.<br /> <br /> ==Chromosome X==<br /> ===--xLabel=== <br /> * --xLabel takes a string that used as label for chromosome X in your file. <br /> * The default is &quot;X&quot;.<br /> <br /> ===--xStart=== <br /> * --xStart takes an integer that described the start position of nonPAR region on chromosome X.<br /> * The default is 2699520 based on Human Genome build 19.<br /> <br /> ===--xEnd===<br /> * --xStart takes an integer that described the end position of nonPAR region on chromosome X.<br /> * The default is 154931044 based on Human Genome build 19.<br /> <br /> ==Others==<br /> ===--cpu[1]=== <br /> *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes.<br /> <br /> ===--kinOnly===<br /> *--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set.<br /> *To also estimate chromosome X kinship, --vcX option should be added in command line.<br /> <br /> ===--geneMap===<br /> * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. <br /> * The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.<br /> <br /> ===--mergedVCFID===<br /> * This options allows RAREMETALWORKER to recognize VCF samples IDs in &quot;FAMID_PID&quot; format. <br /> * The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file.<br /> <br /> ==PhoneHome==<br /> * See [[PhoneHome]] for more information on how PhoneHome works and what it does.<br /> ===--noPhoneHome===<br /> * --noPhoneHome disables PhoneHome. <br /> * PhoneHome is enabled by default based on the thinning parameter.<br /> ===--phoneHomeThinning===<br /> * --phoneHomeThinning (0-100) adjusts the frequency of PhoneHome.<br /> * The default is 100, running 100% of the time.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETALWORKER_command_reference&diff=12971 RAREMETALWORKER command reference 2015-03-09T06:14:41Z <p>Shuang Feng: /* --dosage */</p> <hr /> <div>==Useful Links==<br /> <br /> Here are some useful links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]<br /> * The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]<br /> * The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']]<br /> * The [[RAREMETAL_FAQ | '''FAQ''']]<br /> <br /> Options:<br /> Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],<br /> --noeof<br /> Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,<br /> --labelHits<br /> VC Options : --vcX, --separateX<br /> Trait Options : --makeResiduals, --inverseNormal, --traitName []<br /> Model Options : --recessive, --dominant<br /> Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],<br /> --kinSave<br /> Kinship Options : --kinMaf [0.05], --kinMiss [0.05]<br /> Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],<br /> --maleLabel [1], --femaleLabel [2]<br /> others : --cpu [1], --kinOnly,<br /> --geneMap [../data/refFlat_hg19.txt], --mergedVCFID<br /> PhoneHome : --noPhoneHome, --phoneHomeThinning [100]<br /> <br /> ==Input Files==<br /> ===--ped===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format PED''']] file name.<br /> ===--dat===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format DAT''']] file name.<br /> ===--vcf===<br /> *--vcf takes a string of your [[RAREMETALWORKER#VCF_File | '''VCF''']] file name.<br /> ===--dosage===<br /> * When --dosage is issued in command line, RAREMETALWORKER reads dosage from your [[RAREMETALWORKER#VCF_File | '''VCF''']] file.<br /> * --dosage must be used with --vcf option.<br /> * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']].<br /> <br /> ===--flagDosage===<br /> * This option let user customize the name of field in VCF file that labels dosage data.<br /> * The default is &quot;DS&quot;.<br /> <br /> ===--noeof===<br /> * If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file. <br /> * Please see [[RAREMETAL_FAQ#error:_BGZF_EOF_marker_is_missing_in_xxx.vcf.gz | '''BGZF EOF''']] for more details.<br /> <br /> ==Output Files==<br /> <br /> ===--prefix===<br /> * --prefix takes a value of a string as the prefix of your output files. <br /> * For a full list of output files generated by RAREMETALWORKER, please refer to [[RAREMETALWORKER#OUTPUT_FILE_FORMATS | '''output''']].<br /> <br /> ===--LDwindow===<br /> *--LDwindow takes a integer value as the size of the moving window. <br /> * RAREMETALWORKER generates LD matrices between a current marker that it is working on and all markers within this window.<br /> * The default size is 1 million bases.<br /> * For more information about the LD matrix, please refer to [[RAREMETALWORKER#LD_Matrices | '''LD matrix''']].<br /> <br /> ===--zip===<br /> * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. <br /> <br /> === --thin ===<br /> * If --thin is issued, then RAREMETALWORKER generates [[RAREMETALWORKER#Plots | '''QQ plots and Manhattan plots''']] with less resolution (points), to make the pdf files smaller in size.<br /> <br /> ===--labelHits===<br /> * If --thin is issued, then RAREMETALWORKER automatically label the loci that are above a threshold.<br /> * The threshold is calculated using Bonferroni correction (''0.05/N, where N is the total number of polymorphic markers'').<br /> <br /> ==VC Options==<br /> <br /> ===--vcX===<br /> * --vcX option has to be used with --kinPedigree (when pedigree kinship is used), or --kinGeno (when genomic relationship matrix is estimated), or --kinFile ( when GRM is read from a file). <br /> * Using --vcX option let RAREMETALWORKER fit a linear mixed model to analyze chromosome X, using both autosomal kinship and chromosome X kinship. <br /> <br /> ===--separateX===<br /> * --separateX option must be used with --vcX option. <br /> * Using --separateX option requests RAREMETALWORKER to fit a linear mixed model using only chromosome X kinship for analyses of chromosome X markers. <br /> <br /> Please refer to [[RAREMETALWORKER_method#ANALYZING_MARKERS_ON_CHROMOSOME_X| '''method''']] and [[RAREMETALWORKER_SPECIAL_TOPICS#Analyzing_Chromosome_X | '''technical details''']] for more explanation.<br /> <br /> ==Trait Options==<br /> ===--makeResiduals===<br /> * If --makeResiduals is used, then covariates are adjusted before fitting linear models using residuals.<br /> <br /> ===--inverseNormal===<br /> * If --inverseNormal is used, but not with --makeResiduals, then trait values are inverse normalized before fitting linear models.<br /> * If --inverseNormal and --makeResiduals are used together, then covariates are adjusted and inverse normalized residuals are used to fit linear models. <br /> <br /> ===--traitName===<br /> * --traitName takes a string of the trait name that you want to analyze. <br /> * If this option is not used, then all traits included in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED/DAT''']] files are analyzed.<br /> <br /> ==Model Options==<br /> ===--recessive===<br /> * If --recessive is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''recessive output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.recessive.plots.pdf''.<br /> ===--dominant===<br /> * If --dominant is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''dominant output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.dominant.plots.pdf''.<br /> <br /> ==Kinship Source==<br /> ===--kinPedigree===<br /> * If --kinPedigree is used, pedigree structure coded in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file is used to generate a kinship matrix for later fitting linear mixed model before associations. <br /> <br /> ===--kinGeno===<br /> * If --kinPedigree is used, then a genomic relationship matrix is estimated from genotype. <br /> * If --vcX option is used, then a separate genomic relationship matrix for chromosome X is also estimated. <br /> * For details about how to estimate GRM, please refer to [[RAREMETALWORKER_method#MODELING_RELATEDNESS | ''methods''']].<br /> <br /> ===--kinFile===<br /> * --kinFile takes a string of the file name of previously saved GRM with format described in [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> * This option reads GRM from the file and then extract the correct GRM based on samples to be analyzed according to your specifications, such as traits to be analyzed, missing covariates and genotypes (please refer to [[RAREMETALWORKER_SPECIAL_TOPICS#Missing_Data | '''missing data''']] for more details).<br /> * --kinFile can not be used together with --kinGeno. <br /> <br /> ===--kinxFile===<br /> * --kinxFile must be used with --kinFile and --vcX. <br /> * --kinxFile takes a string of file name of the previously saved GRM for chromosome X. <br /> * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur.<br /> ===--kinSave===<br /> * This option must be used with --kinGeno.<br /> * Issuing --kinSave will request [[RAREMETALWORKER]] to store the estimated GMR in a file named yourprefix.Empirical.Kinship.gz.<br /> * If --vcX is also issued in the command line, then a separate file named yourprefix.Empirical.KinshipX.gz will be generated where the GRM of chromosome X is saved.<br /> *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> <br /> ==Kinship Options==<br /> ===--kinMaf=== <br /> * --kinMaf takes a value that specifies the MAF cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with MAF&lt;0.05 are not used for estimating GRMs.<br /> ===--kinMiss===<br /> * --kinMiss takes a value that specifies the missing genotype cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with genotype call rate &lt;0.95 are not used for estimating GRMs.<br /> <br /> ==Chromosome X==<br /> ===--xLabel=== <br /> * --xLabel takes a string that used as label for chromosome X in your file. <br /> * The default is &quot;X&quot;.<br /> <br /> ===--xStart=== <br /> * --xStart takes an integer that described the start position of nonPAR region on chromosome X.<br /> * The default is 2699520 based on Human Genome build 19.<br /> <br /> ===--xEnd===<br /> * --xStart takes an integer that described the end position of nonPAR region on chromosome X.<br /> * The default is 154931044 based on Human Genome build 19.<br /> <br /> ==Others==<br /> ===--cpu[1]=== <br /> *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes.<br /> <br /> ===--kinOnly===<br /> *--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set.<br /> *To also estimate chromosome X kinship, --vcX option should be added in command line.<br /> <br /> ===--geneMap===<br /> * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. <br /> * The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.<br /> <br /> ==PhoneHome==<br /> * See [[PhoneHome]] for more information on how PhoneHome works and what it does.<br /> ===--noPhoneHome===<br /> * --noPhoneHome disables PhoneHome. <br /> * PhoneHome is enabled by default based on the thinning parameter.<br /> ===--phoneHomeThinning===<br /> * --phoneHomeThinning (0-100) adjusts the frequency of PhoneHome.<br /> * The default is 100, running 100% of the time.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREMETALWORKER_command_reference&diff=12970 RAREMETALWORKER command reference 2015-03-09T06:13:28Z <p>Shuang Feng: /* Useful Links */</p> <hr /> <div>==Useful Links==<br /> <br /> Here are some useful links to key pages:<br /> * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]<br /> * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]<br /> * The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]<br /> * The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']]<br /> * The [[RAREMETAL_FAQ | '''FAQ''']]<br /> <br /> Options:<br /> Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],<br /> --noeof<br /> Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,<br /> --labelHits<br /> VC Options : --vcX, --separateX<br /> Trait Options : --makeResiduals, --inverseNormal, --traitName []<br /> Model Options : --recessive, --dominant<br /> Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],<br /> --kinSave<br /> Kinship Options : --kinMaf [0.05], --kinMiss [0.05]<br /> Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],<br /> --maleLabel [1], --femaleLabel [2]<br /> others : --cpu [1], --kinOnly,<br /> --geneMap [../data/refFlat_hg19.txt], --mergedVCFID<br /> PhoneHome : --noPhoneHome, --phoneHomeThinning [100]<br /> <br /> ==Input Files==<br /> ===--ped===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format PED''']] file name.<br /> ===--dat===<br /> *--ped takes a string of your [[RAREMETALWORKER#PED_and_DAT_Files | '''MERLIN format DAT''']] file name.<br /> ===--vcf===<br /> *--vcf takes a string of your [[RAREMETALWORKER#VCF_File | '''VCF''']] file name.<br /> ===--dosage===<br /> * When --dosage is issued in command line, RAREMETALWORKER reads dosage from your [[RAREMETALWORKER#VCF_File | '''VCF''']] file.<br /> * --dosage must be used with --vcf option.<br /> * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']].<br /> ===--noeof===<br /> * If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file. <br /> * Please see [[RAREMETAL_FAQ#error:_BGZF_EOF_marker_is_missing_in_xxx.vcf.gz | '''BGZF EOF''']] for more details.<br /> <br /> ==Output Files==<br /> <br /> ===--prefix===<br /> * --prefix takes a value of a string as the prefix of your output files. <br /> * For a full list of output files generated by RAREMETALWORKER, please refer to [[RAREMETALWORKER#OUTPUT_FILE_FORMATS | '''output''']].<br /> <br /> ===--LDwindow===<br /> *--LDwindow takes a integer value as the size of the moving window. <br /> * RAREMETALWORKER generates LD matrices between a current marker that it is working on and all markers within this window.<br /> * The default size is 1 million bases.<br /> * For more information about the LD matrix, please refer to [[RAREMETALWORKER#LD_Matrices | '''LD matrix''']].<br /> <br /> ===--zip===<br /> * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. <br /> <br /> === --thin ===<br /> * If --thin is issued, then RAREMETALWORKER generates [[RAREMETALWORKER#Plots | '''QQ plots and Manhattan plots''']] with less resolution (points), to make the pdf files smaller in size.<br /> <br /> ===--labelHits===<br /> * If --thin is issued, then RAREMETALWORKER automatically label the loci that are above a threshold.<br /> * The threshold is calculated using Bonferroni correction (''0.05/N, where N is the total number of polymorphic markers'').<br /> <br /> ==VC Options==<br /> <br /> ===--vcX===<br /> * --vcX option has to be used with --kinPedigree (when pedigree kinship is used), or --kinGeno (when genomic relationship matrix is estimated), or --kinFile ( when GRM is read from a file). <br /> * Using --vcX option let RAREMETALWORKER fit a linear mixed model to analyze chromosome X, using both autosomal kinship and chromosome X kinship. <br /> <br /> ===--separateX===<br /> * --separateX option must be used with --vcX option. <br /> * Using --separateX option requests RAREMETALWORKER to fit a linear mixed model using only chromosome X kinship for analyses of chromosome X markers. <br /> <br /> Please refer to [[RAREMETALWORKER_method#ANALYZING_MARKERS_ON_CHROMOSOME_X| '''method''']] and [[RAREMETALWORKER_SPECIAL_TOPICS#Analyzing_Chromosome_X | '''technical details''']] for more explanation.<br /> <br /> ==Trait Options==<br /> ===--makeResiduals===<br /> * If --makeResiduals is used, then covariates are adjusted before fitting linear models using residuals.<br /> <br /> ===--inverseNormal===<br /> * If --inverseNormal is used, but not with --makeResiduals, then trait values are inverse normalized before fitting linear models.<br /> * If --inverseNormal and --makeResiduals are used together, then covariates are adjusted and inverse normalized residuals are used to fit linear models. <br /> <br /> ===--traitName===<br /> * --traitName takes a string of the trait name that you want to analyze. <br /> * If this option is not used, then all traits included in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED/DAT''']] files are analyzed.<br /> <br /> ==Model Options==<br /> ===--recessive===<br /> * If --recessive is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''recessive output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.recessive.plots.pdf''.<br /> ===--dominant===<br /> * If --dominant is used, then RAREMETALWORKER generates recessive results in addition to the additive results. <br /> * The set of association results generated by default can be found in [[RAREMETALWORKER#OUTPUT_FILE_NAMES | '''dominant output''']].<br /> * A separate pdf file with QQ and Manhattan plots based on recessive results is generated with name ''yourprefix.traitname.dominant.plots.pdf''.<br /> <br /> ==Kinship Source==<br /> ===--kinPedigree===<br /> * If --kinPedigree is used, pedigree structure coded in [[RAREMETALWORKER#PED_and_DAT_Files | '''PED''']] file is used to generate a kinship matrix for later fitting linear mixed model before associations. <br /> <br /> ===--kinGeno===<br /> * If --kinPedigree is used, then a genomic relationship matrix is estimated from genotype. <br /> * If --vcX option is used, then a separate genomic relationship matrix for chromosome X is also estimated. <br /> * For details about how to estimate GRM, please refer to [[RAREMETALWORKER_method#MODELING_RELATEDNESS | ''methods''']].<br /> <br /> ===--kinFile===<br /> * --kinFile takes a string of the file name of previously saved GRM with format described in [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> * This option reads GRM from the file and then extract the correct GRM based on samples to be analyzed according to your specifications, such as traits to be analyzed, missing covariates and genotypes (please refer to [[RAREMETALWORKER_SPECIAL_TOPICS#Missing_Data | '''missing data''']] for more details).<br /> * --kinFile can not be used together with --kinGeno. <br /> <br /> ===--kinxFile===<br /> * --kinxFile must be used with --kinFile and --vcX. <br /> * --kinxFile takes a string of file name of the previously saved GRM for chromosome X. <br /> * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur.<br /> ===--kinSave===<br /> * This option must be used with --kinGeno.<br /> * Issuing --kinSave will request [[RAREMETALWORKER]] to store the estimated GMR in a file named yourprefix.Empirical.Kinship.gz.<br /> * If --vcX is also issued in the command line, then a separate file named yourprefix.Empirical.KinshipX.gz will be generated where the GRM of chromosome X is saved.<br /> *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']].<br /> <br /> ==Kinship Options==<br /> ===--kinMaf=== <br /> * --kinMaf takes a value that specifies the MAF cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with MAF&lt;0.05 are not used for estimating GRMs.<br /> ===--kinMiss===<br /> * --kinMiss takes a value that specifies the missing genotype cutoff for variants to be used to estimate GRMs.<br /> * The default is 0.05, which means variants with genotype call rate &lt;0.95 are not used for estimating GRMs.<br /> <br /> ==Chromosome X==<br /> ===--xLabel=== <br /> * --xLabel takes a string that used as label for chromosome X in your file. <br /> * The default is &quot;X&quot;.<br /> <br /> ===--xStart=== <br /> * --xStart takes an integer that described the start position of nonPAR region on chromosome X.<br /> * The default is 2699520 based on Human Genome build 19.<br /> <br /> ===--xEnd===<br /> * --xStart takes an integer that described the end position of nonPAR region on chromosome X.<br /> * The default is 154931044 based on Human Genome build 19.<br /> <br /> ==Others==<br /> ===--cpu[1]=== <br /> *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes.<br /> <br /> ===--kinOnly===<br /> *--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set.<br /> *To also estimate chromosome X kinship, --vcX option should be added in command line.<br /> <br /> ===--geneMap===<br /> * --geneMap takes a string describing the path to find mapping file for manhattan plot annotation. <br /> * The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.<br /> <br /> ==PhoneHome==<br /> * See [[PhoneHome]] for more information on how PhoneHome works and what it does.<br /> ===--noPhoneHome===<br /> * --noPhoneHome disables PhoneHome. <br /> * PhoneHome is enabled by default based on the thinning parameter.<br /> ===--phoneHomeThinning===<br /> * --phoneHomeThinning (0-100) adjusts the frequency of PhoneHome.<br /> * The default is 100, running 100% of the time.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12908 RAREFY TUTORIAL 2015-02-17T09:10:15Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.<br /> <br /> ==COMMAND==<br /> *Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.<br /> rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1<br /> <br /> ==OUTPUT==<br /> *Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in &quot;sim1_simul_rarefy.trait.Decreasing.result&quot; and &quot;sim1_simul_rarefy.trait.Increasing.result&quot; separately.<br /> *Use the following command to sort the RAREFY score to select informative individuals:<br /> sort -k7 -gr sim1_simul_rarefy.trait.Increasing.result | head -10<br /> *The top 10 selected individuals are:<br /> famid pid fatid motid sex residual rarefy_idv_score rarefy_fam_score<br /> 1994 5 1 2 1 4.05563 0.839037 2.73226<br /> 1994 2 0 0 2 3.66226 0.829384 2.73226<br /> 345 1 0 0 1 3.45514 0.785963 1.95526<br /> 345 4 1 2 2 3.20513 0.782924 1.95526<br /> 3503 4 1 2 2 3.33598 0.621358 1.85789<br /> 3503 1 0 0 1 2.15643 0.619741 1.85789<br /> 1994 3 1 2 1 2.25633 0.607197 2.73226<br /> 3503 5 1 2 1 2.51068 0.601241 1.85789<br /> 1994 4 1 2 2 1.85392 0.437127 2.73226<br /> 3860 2 0 0 2 2.45598 0.405228 1.5474</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_COMMAND&diff=12907 RAREFY COMMAND 2015-02-17T09:09:11Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==RAREFY COMMANDS==<br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> ==Input Files==<br /> ===--ped [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.<br /> <br /> ===--dat [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file.<br /> <br /> ==Methods==<br /> ===--MCMC [on|off]===<br /> default is '''off''', but will be automatically turned on for families larger than 25 individuals.<br /> <br /> ===--traitIncreasing [on|off]===<br /> default is '''off'''; can be used together with '''--traitDecreasing''' options or used alone.<br /> ===--traitDecreasing [on|off]=== <br /> default is '''off'''; can be used together with '''--traitIncreasing''' options or used alone.<br /> <br /> ==Trait==<br /> ===--inverseNormal [on|off]===<br /> default is '''off'''; '''on''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). <br /> ===--useCovariates [on|off]===<br /> default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with &quot;C&quot; in DAT file). <br /> ===--traitName [string]===<br /> default is to analyze all traits saved in PED/DAT file (traits are labeled with &quot;T&quot; in DAT file).<br /> <br /> ==Parameters==<br /> ===--maf [double]===<br /> default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.<br /> <br /> ===--effect [double]===<br /> default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.<br /> <br /> ==MCMC==<br /> ===--seed [int]===<br /> ===--chains [int]===<br /> The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. <br /> ===--iterations [int]===<br /> The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.<br /> <br /> ==Others==<br /> ===--famList [string]===<br /> This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--famID [string]===<br /> This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--cpus [int]===<br /> This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.<br /> NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.<br /> <br /> ===--prefix [string]===<br /> This option allows users to customize the output prefix generated by RAREFY.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOCUMENTATION&diff=12906 RAREFY DOCUMENTATION 2015-02-17T09:08:59Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']]<br /> * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==KEY FEATURES==<br /> <br /> *'''RAREFY''' is a likelihood-based method to prioritize individuals in family AND population samples. <br /> <br /> *'''RAREFY''' takes account familial relatedness and allows adjusting covariates.<br /> <br /> *'''RAREFY''' is able to handle large and complex pedigrees.<br /> <br /> ==DOWNLOAD &amp; BUILD==<br /> Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables.<br /> <br /> ==INPUT FORMAT==<br /> *'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed.<br /> *Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.<br /> <br /> ==OUTPUT FORMAT==<br /> '''RAREFY''' generates output file with eight columns.<br /> <br /> ==SOFTWARE INTERFACE==<br /> <br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples.<br /> <br /> ==EXAMPLES==<br /> *To prioritize individuals likely to be carriers of trait-increasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix<br /> *To prioritize individuals likely to be carriers of trait-decreasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix<br /> *To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --prefix your.output.prefix<br /> *To analyze families using MCMC method in 3 chains and 50000000 iterations:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix<br /> *To inverse Normalize the phenotype before analysis:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix <br /> *To inverse Normalize the phenotype and then adjust covariates saved in PED/DAT file before RAREFY analysis:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --useCovariates --prefix your.output.prefix<br /> *To analyze only a subset of families in the sample:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix <br /> NOTE: although only the subset of families will be &quot;RAREFIED&quot;, all samples saved in your.ped will be used to fit variance component model.<br /> *To analyze only one family:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix<br /> NOTE: although only the family included in --famID will be &quot;RAREFIED&quot;, all samples saved in your.ped will be used to fit variance component model.<br /> *To analyze only one trait saved in your.ped and your.dat file:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --traitName LDL --prefix your.output.prefix</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12905 RAREFY DOWNLOAD 2015-02-17T09:08:41Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12904 RAREFY DOWNLOAD 2015-02-17T09:08:22Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_TUTORIAL | '''RAREFY Tutorial''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12903 RAREFY TUTORIAL 2015-02-17T08:33:01Z <p>Shuang Feng: /* OUTPUT */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.<br /> <br /> ==COMMAND==<br /> *Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.<br /> rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1<br /> <br /> ==OUTPUT==<br /> *Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in &quot;sim1_simul_rarefy.trait.Decreasing.result&quot; and &quot;sim1_simul_rarefy.trait.Increasing.result&quot; separately.<br /> *Use the following command to sort the RAREFY score to select informative individuals:<br /> sort -k7 -gr sim1_simul_rarefy.trait.Increasing.result | head -10<br /> *The top 10 selected individuals are:<br /> famid pid fatid motid sex residual rarefy_idv_score rarefy_fam_score<br /> 1994 5 1 2 1 4.05563 0.839037 2.73226<br /> 1994 2 0 0 2 3.66226 0.829384 2.73226<br /> 345 1 0 0 1 3.45514 0.785963 1.95526<br /> 345 4 1 2 2 3.20513 0.782924 1.95526<br /> 3503 4 1 2 2 3.33598 0.621358 1.85789<br /> 3503 1 0 0 1 2.15643 0.619741 1.85789<br /> 1994 3 1 2 1 2.25633 0.607197 2.73226<br /> 3503 5 1 2 1 2.51068 0.601241 1.85789<br /> 1994 4 1 2 2 1.85392 0.437127 2.73226<br /> 3860 2 0 0 2 2.45598 0.405228 1.5474</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12902 RAREFY TUTORIAL 2015-02-17T08:29:08Z <p>Shuang Feng: /* OUTPUT */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.<br /> <br /> ==COMMAND==<br /> *Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.<br /> rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1<br /> <br /> ==OUTPUT==<br /> *Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in &quot;sim1_simul_rarefy.trait.Decreasing.result&quot; and &quot;sim1_simul_rarefy.trait.Decreasing.result&quot; separately.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12901 RAREFY TUTORIAL 2015-02-17T08:27:39Z <p>Shuang Feng: /* COMMAND */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.<br /> <br /> ==COMMAND==<br /> *Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.<br /> rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12900 RAREFY TUTORIAL 2015-02-17T08:25:26Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12899 RAREFY TUTORIAL 2015-02-17T08:24:45Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12898 RAREFY TUTORIAL 2015-02-17T08:23:02Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12897 RAREFY TUTORIAL 2015-02-17T08:22:52Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[File:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12896 RAREFY TUTORIAL 2015-02-17T08:22:33Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the [[rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:Rarefy.example.tar.gz&diff=12895 File:Rarefy.example.tar.gz 2015-02-17T08:22:05Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12894 RAREFY TUTORIAL 2015-02-17T07:47:35Z <p>Shuang Feng: /* EXAMPLE DATA SET */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *Please download the PED and DAT file to your computer.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_TUTORIAL&diff=12893 RAREFY TUTORIAL 2015-02-17T07:46:48Z <p>Shuang Feng: Created page with &quot;== Useful Wiki Pages == * The &#039;&#039;&#039;RAREFY Homepage&#039;&#039;&#039; * The &#039;&#039;&#039;RAREFY Documentation&#039;&#039;&#039; * The &#039;&#039;&#039;RAREFY COMMAND REFERENCE&#039;&#039;&#039; *...&quot;</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==EXAMPLE DATA SET==<br /> *To to uploaded.<br /> <br /> ==COMMAND==<br /> <br /> ==OUTPUT==</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_FAQ&diff=12891 RAREFY FAQ 2015-02-17T07:44:36Z <p>Shuang Feng: /* Q1. Could RAREFY prioritize individuals in population samples? */</p> <hr /> <div>==Q1. Could RAREFY prioritize individuals in population samples?==<br /> <br /> ===Yes. If individuals are coded as unrelated in your PED file, RAREFY considers it as a population sample of unrelated individuals.===</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_FAQ&diff=12890 RAREFY FAQ 2015-02-17T07:44:23Z <p>Shuang Feng: /* Q1. Could RAREFY prioritize individuals in population samples? */</p> <hr /> <div>==Q1. Could RAREFY prioritize individuals in population samples?==<br /> <br /> ===ANSWER: Yes. If individuals are coded as unrelated in your PED file, RAREFY considers it as a population sample of unrelated individuals.===</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_FAQ&diff=12889 RAREFY FAQ 2015-02-17T07:44:06Z <p>Shuang Feng: /* Q1. Could RAREFY prioritize individuals in population samples? */</p> <hr /> <div>==Q1. Could RAREFY prioritize individuals in population samples?==<br /> <br /> *ANSWER: Yes. If individuals are coded as unrelated in your PED file, RAREFY considers it as a population sample of unrelated individuals.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_FAQ&diff=12888 RAREFY FAQ 2015-02-17T07:43:45Z <p>Shuang Feng: Created page with &quot;==Q1. Could RAREFY prioritize individuals in population samples?== Yes. If individuals are coded as unrelated in your PED file, RAREFY considers it as a population sample of...&quot;</p> <hr /> <div>==Q1. Could RAREFY prioritize individuals in population samples?==<br /> <br /> Yes. If individuals are coded as unrelated in your PED file, RAREFY considers it as a population sample of unrelated individuals.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOCUMENTATION&diff=12887 RAREFY DOCUMENTATION 2015-02-17T07:41:40Z <p>Shuang Feng: </p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==KEY FEATURES==<br /> <br /> *'''RAREFY''' is a likelihood-based method to prioritize individuals in family AND population samples. <br /> <br /> *'''RAREFY''' takes account familial relatedness and allows adjusting covariates.<br /> <br /> *'''RAREFY''' is able to handle large and complex pedigrees.<br /> <br /> ==DOWNLOAD &amp; BUILD==<br /> Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables.<br /> <br /> ==INPUT FORMAT==<br /> *'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed.<br /> *Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.<br /> <br /> ==OUTPUT FORMAT==<br /> '''RAREFY''' generates output file with eight columns.<br /> <br /> ==SOFTWARE INTERFACE==<br /> <br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples.<br /> <br /> ==EXAMPLES==<br /> *To prioritize individuals likely to be carriers of trait-increasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix<br /> *To prioritize individuals likely to be carriers of trait-decreasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix<br /> *To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --prefix your.output.prefix<br /> *To analyze families using MCMC method in 3 chains and 50000000 iterations:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix<br /> *To inverse Normalize the phenotype before analysis:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix <br /> *To inverse Normalize the phenotype and then adjust covariates saved in PED/DAT file before RAREFY analysis:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --useCovariates --prefix your.output.prefix<br /> *To analyze only a subset of families in the sample:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix <br /> NOTE: although only the subset of families will be &quot;RAREFIED&quot;, all samples saved in your.ped will be used to fit variance component model.<br /> *To analyze only one family:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix<br /> NOTE: although only the family included in --famID will be &quot;RAREFIED&quot;, all samples saved in your.ped will be used to fit variance component model.<br /> *To analyze only one trait saved in your.ped and your.dat file:<br /> rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --traitName LDL --prefix your.output.prefix</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_COMMAND&diff=12886 RAREFY COMMAND 2015-02-17T07:40:42Z <p>Shuang Feng: /* --ped [string] */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==RAREFY COMMANDS==<br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> ==Input Files==<br /> ===--ped [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.<br /> <br /> ===--dat [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file.<br /> <br /> ==Methods==<br /> ===--MCMC [on|off]===<br /> default is '''off''', but will be automatically turned on for families larger than 25 individuals.<br /> <br /> ===--traitIncreasing [on|off]===<br /> default is '''off'''; can be used together with '''--traitDecreasing''' options or used alone.<br /> ===--traitDecreasing [on|off]=== <br /> default is '''off'''; can be used together with '''--traitIncreasing''' options or used alone.<br /> <br /> ==Trait==<br /> ===--inverseNormal [on|off]===<br /> default is '''off'''; '''on''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). <br /> ===--useCovariates [on|off]===<br /> default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with &quot;C&quot; in DAT file). <br /> ===--traitName [string]===<br /> default is to analyze all traits saved in PED/DAT file (traits are labeled with &quot;T&quot; in DAT file).<br /> <br /> ==Parameters==<br /> ===--maf [double]===<br /> default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.<br /> <br /> ===--effect [double]===<br /> default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.<br /> <br /> ==MCMC==<br /> ===--seed [int]===<br /> ===--chains [int]===<br /> The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. <br /> ===--iterations [int]===<br /> The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.<br /> <br /> ==Others==<br /> ===--famList [string]===<br /> This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--famID [string]===<br /> This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--cpus [int]===<br /> This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.<br /> NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.<br /> <br /> ===--prefix [string]===<br /> This option allows users to customize the output prefix generated by RAREFY.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_COMMAND&diff=12885 RAREFY COMMAND 2015-02-17T07:40:32Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY Download Page''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==RAREFY COMMANDS==<br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> ==Input Files==<br /> ===--ped [string]===<br /> followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.<br /> <br /> ===--dat [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file.<br /> <br /> ==Methods==<br /> ===--MCMC [on|off]===<br /> default is '''off''', but will be automatically turned on for families larger than 25 individuals.<br /> <br /> ===--traitIncreasing [on|off]===<br /> default is '''off'''; can be used together with '''--traitDecreasing''' options or used alone.<br /> ===--traitDecreasing [on|off]=== <br /> default is '''off'''; can be used together with '''--traitIncreasing''' options or used alone.<br /> <br /> ==Trait==<br /> ===--inverseNormal [on|off]===<br /> default is '''off'''; '''on''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). <br /> ===--useCovariates [on|off]===<br /> default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with &quot;C&quot; in DAT file). <br /> ===--traitName [string]===<br /> default is to analyze all traits saved in PED/DAT file (traits are labeled with &quot;T&quot; in DAT file).<br /> <br /> ==Parameters==<br /> ===--maf [double]===<br /> default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.<br /> <br /> ===--effect [double]===<br /> default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.<br /> <br /> ==MCMC==<br /> ===--seed [int]===<br /> ===--chains [int]===<br /> The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. <br /> ===--iterations [int]===<br /> The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.<br /> <br /> ==Others==<br /> ===--famList [string]===<br /> This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--famID [string]===<br /> This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--cpus [int]===<br /> This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.<br /> NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.<br /> <br /> ===--prefix [string]===<br /> This option allows users to customize the output prefix generated by RAREFY.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_COMMAND&diff=12884 RAREFY COMMAND 2015-02-17T07:40:16Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Home''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY DOWNLOAD PAGE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==RAREFY COMMANDS==<br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> ==Input Files==<br /> ===--ped [string]===<br /> followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.<br /> <br /> ===--dat [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file.<br /> <br /> ==Methods==<br /> ===--MCMC [on|off]===<br /> default is '''off''', but will be automatically turned on for families larger than 25 individuals.<br /> <br /> ===--traitIncreasing [on|off]===<br /> default is '''off'''; can be used together with '''--traitDecreasing''' options or used alone.<br /> ===--traitDecreasing [on|off]=== <br /> default is '''off'''; can be used together with '''--traitIncreasing''' options or used alone.<br /> <br /> ==Trait==<br /> ===--inverseNormal [on|off]===<br /> default is '''off'''; '''on''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). <br /> ===--useCovariates [on|off]===<br /> default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with &quot;C&quot; in DAT file). <br /> ===--traitName [string]===<br /> default is to analyze all traits saved in PED/DAT file (traits are labeled with &quot;T&quot; in DAT file).<br /> <br /> ==Parameters==<br /> ===--maf [double]===<br /> default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.<br /> <br /> ===--effect [double]===<br /> default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.<br /> <br /> ==MCMC==<br /> ===--seed [int]===<br /> ===--chains [int]===<br /> The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. <br /> ===--iterations [int]===<br /> The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.<br /> <br /> ==Others==<br /> ===--famList [string]===<br /> This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--famID [string]===<br /> This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--cpus [int]===<br /> This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.<br /> NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.<br /> <br /> ===--prefix [string]===<br /> This option allows users to customize the output prefix generated by RAREFY.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_COMMAND&diff=12883 RAREFY COMMAND 2015-02-17T07:40:03Z <p>Shuang Feng: </p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_DOWNLOAD | '''RAREFY DOWNLOAD PAGE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==RAREFY COMMANDS==<br /> Options:<br /> Input Files : --ped [], --dat []<br /> Methods : --MCMC, --traitIncreasing, --traitDecreasing<br /> Trait : --inverseNormal, --useCovariates, --traitName []<br /> Parameters : --maf [1.0e-03], --effect [1.00]<br /> MCMC : --seed, --chains [3], --iterations [50000000]<br /> Other : --famList [], --famID [], --cpus [5], --prefix []<br /> <br /> ==Input Files==<br /> ===--ped [string]===<br /> followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.<br /> <br /> ===--dat [string]===<br /> followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format DAT] file.<br /> <br /> ==Methods==<br /> ===--MCMC [on|off]===<br /> default is '''off''', but will be automatically turned on for families larger than 25 individuals.<br /> <br /> ===--traitIncreasing [on|off]===<br /> default is '''off'''; can be used together with '''--traitDecreasing''' options or used alone.<br /> ===--traitDecreasing [on|off]=== <br /> default is '''off'''; can be used together with '''--traitIncreasing''' options or used alone.<br /> <br /> ==Trait==<br /> ===--inverseNormal [on|off]===<br /> default is '''off'''; '''on''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). <br /> ===--useCovariates [on|off]===<br /> default is '''off'''; '''on''' will adjust any covariates saved in PED/DAT file (covariates are labeled with &quot;C&quot; in DAT file). <br /> ===--traitName [string]===<br /> default is to analyze all traits saved in PED/DAT file (traits are labeled with &quot;T&quot; in DAT file).<br /> <br /> ==Parameters==<br /> ===--maf [double]===<br /> default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.<br /> <br /> ===--effect [double]===<br /> default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.<br /> <br /> ==MCMC==<br /> ===--seed [int]===<br /> ===--chains [int]===<br /> The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains. <br /> ===--iterations [int]===<br /> The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.<br /> <br /> ==Others==<br /> ===--famList [string]===<br /> This options allows analysis of only a subset of families listed in a file. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--famID [string]===<br /> This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.<br /> ===--cpus [int]===<br /> This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.<br /> NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD | '''COMPILE''']] for more information.<br /> <br /> ===--prefix [string]===<br /> This option allows users to customize the output prefix generated by RAREFY.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12882 RAREFY DOWNLOAD 2015-02-17T07:39:03Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12881 RAREFY DOWNLOAD 2015-02-17T07:38:28Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_COMMAND_REFERENCE | '''RAREFY COMMAND REFERENCE''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12880 RAREFY DOWNLOAD 2015-02-17T07:37:53Z <p>Shuang Feng: /* Useful Wiki Pages */</p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_DOC | '''RAREFY Documentation''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> <br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12879 RAREFY DOWNLOAD 2015-02-17T07:37:17Z <p>Shuang Feng: </p> <hr /> <div>== Useful Wiki Pages ==<br /> <br /> * The [[RAREFY | '''RAREFY Homepage''']]<br /> * The [[RAREFY_Documentation | '''RAREFY documentation''']]<br /> * The [[RAREFY_FAQ | '''FAQ''']]<br /> ==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12878 RAREFY DOWNLOAD 2015-02-17T07:35:22Z <p>Shuang Feng: /* EXECUTABLES */</p> <hr /> <div>==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[Media:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12877 RAREFY DOWNLOAD 2015-02-17T07:35:00Z <p>Shuang Feng: /* EXECUTABLES */</p> <hr /> <div>==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux: [[File:Rarefy1.0.tar.gz | '''RAREFY_1.0_for_Linux''']]<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=File:Rarefy1.0.tar.gz&diff=12876 File:Rarefy1.0.tar.gz 2015-02-17T07:32:51Z <p>Shuang Feng: </p> <hr /> <div></div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12875 RAREFY DOWNLOAD 2015-02-17T07:24:35Z <p>Shuang Feng: /* BUILD */</p> <hr /> <div>==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux:<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.</div> Shuang Feng http://genome.sph.umich.edu/w/index.php?title=RAREFY_DOWNLOAD&diff=12874 RAREFY DOWNLOAD 2015-02-17T07:24:05Z <p>Shuang Feng: /* DOWNLOAD */</p> <hr /> <div>==DOWNLOAD==<br /> ===SOURCE CODE===<br /> Source code is currently available per request. Please contact [[Shuang_Feng | Shuang Feng]] (sfengsph at umich dot edu) for more information.<br /> ===EXECUTABLES===<br /> *For Linux:<br /> <br /> *Executable for Windows and and MAC need to build from source code. Please contact [[Shuang_Feng | Shuang Feng]] for details.<br /> <br /> ==BUILD==</div> Shuang Feng