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From Genome Analysis Wiki
Release 4.15.0; simplify release notes to point to self-contained repository.
[[Category:RAREMETAL]]
[[Category:RAREMETALWORKER]]
== Useful Wiki Pages ==
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL_Change_Log | '''Change Log''']]
== Where to Download =GitHub===
===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 4.13.4 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.4.13.4.tgz prompt> cd raremetal_4.13.4 * If you prefer to build two tools all at once, then do the following: prompt> cd raremetal prompt> make #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. * If you prefer to build individual tool: prompt> cd raremetal/raremetalworker/src prompt> make #This will build RAREMETALWORKER under raremetal/bin/ directory. prompt> cd raremetal/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 raremetal/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.
