View source for RAREMETAL DOWNLOAD & BUILD

== Useful Wiki Pages ==

There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL_Change_Log | Change log]]

== Where to Download ==

===SOURCE CODE===

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.
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:

* [[Media:LINUX_raremetal.4.13.8.tgz ‎|'''for Linux''']] 

Note Mac and Windows versions are still at v4.13.6

* [[Media:MAC_raremetal.4.13.6.tgz ‎|'''for MAC OS X''']]

* [[Media:CYGWIN64_raremetal.4.13.6.tgz ‎|'''for Windows/CygWin64''']]

* [[Media:MINGW_raremetal.4.13.6.tgz ‎|'''for Windows/MinGW''']]

===EXECUTABLES===

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.
*[[Media: Linux_executables_4.13.8.tgz |'''for Linux''']]

===SCRIPTS===

====Calculating Odds Ratio from RAREMETALWORKER output====
*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. 
*The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.

== How to Compile ==

* 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.

* If you choose to build from the source files, you could start from decompress the package using the following command:
  prompt> tar xvf LINUX_raremetal.4.13.8.tgz
  prompt> cd LINUX_raremetal.4.13.8

* If you prefer to build two tools all at once, then do the following:
  prompt> make
  #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. 

* If you prefer to build individual tool:
  prompt> cd LINUX_raremetal.4.13.8/raremetalworker/src
  prompt> make
  #This will build RAREMETALWORKER under raremetal/bin/ directory.

  prompt> cd LINUX_raremetal.4.13.8/raremetal/src
  prompt> make
  #This will build RAREMETAL under raremetal/bin/ directory.

* 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].
  prompt> cd raremetalworker/src
  prompt> make openmp
  #This will build RAREMETALWORKER under raremetal/bin/ directory.

* 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.

==FAQ==

For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.

==Change Log==

===RAREMETALWORKR 4.8 and before===
* Version 0.0.1 was released on 11/13/2012.
* Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)
* Uploaded to public wiki. (11/16/2012)
* Enabled writing log file by defalut. (11/18/2012)
* 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)
* Added HWE pvalue and call rate in summary statistics output. (11/27/2012)
* Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)
* Updated output format. Version 0.0.3 released. (12/3/2012)
* More messages coded into log file. (12/4/2012)
* Version 0.0.4 released. (12/5/2012)
* Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)
* Version 0.0.6 released. (12/6/2012)
* Updated output format for monomorphic sites. (12/7/2012)
* Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)
* Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)
* Fixed a bug when there is missing genotype from VCF file. (2/2013)
* Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)
* Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)
* Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)
* 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)
* Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)
* Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)
* Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)
* Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)
* Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)
* Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.
* Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.
* 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)
* 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.
* Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)
* Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)
* Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)
* 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)

===RAREMETAL 4.8 and before===
* Version 0.0.1 released to U of M CSG group. (2/13/2013)
* Version 0.0.1 released. (2/24/2013)
* Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)
* Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)
* Version 0.3.1 released to fix a bug when one of the alleles coded as missing.
* 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.
* 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.
* Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)
* Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)

===RAREMETAL 4.9 and after===
* 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).
* version 4.11: fixed a bug for inverse-normalizing traits (a bug only in version 4.9 and later).
* version 4.12: improved make file for better compilation.
* version 4.12.1: fixed command interface display issue in raremetalworker.
* 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.
* Version 4.13.1 fixed a bug affecting output format when ped/dat files are used together with --dominant --recessive options.
* 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.
* Version 4.13.3 released to read rvtest output format correctly in raremetal.
* Version 4.13.4 released to store beta estimates of intercept and fixed effects in rarmetalworker *.singlevar.score.txt header.
* Version 4.13.5 released with a bug fixed in conditional analysis in raremetal. (9/29/2014)
* Version 4.13.6 released with a new option --mergedVCFID to recognize VCF files with sample IDs in "FAMID_PID" format, and another new option --flagDosage to flag the field name to label dosage in VCF file. (3/8/2015)
* Version 4.13.7 released. (9/18/2015).
** add --altMAF option.
** generate group file if group from vcf.
** bug fixes in conditional analysis.
** In SKAT meta analysis, skip the variant when all its lambdas are zero.
** tabix RMW output with --zip toggled.
** use -O0 option in compiling. In extremely occasions, gcc optimization will affect the results.