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RAREMETALWORKER (view source)

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'''RAREMETALWORKER''' is a tool for generating summary statistics for rare variants and gene level meta analyses using [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].
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[[Category:RAREMETALWORKER]]
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'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].
    
If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].
 
If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].
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If you have any questions, please contact [[Shuang Feng|'''Shuang Feng''']] sfengsph at umich dot edu or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] goncalo at umich dot edu.
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If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] (goncalo at umich dot edu).
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* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
 
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
 
* The [[RAREMETAL FAQ | '''FAQ''']]
 
* The [[RAREMETAL FAQ | '''FAQ''']]
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* The [[RAREMETAL_Change_Log | '''Change Log''']]
    
== Key Features ==
 
== Key Features ==
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Method description and key formulae can be found in [http://genome.sph.umich.edu/wiki/RAREMETALWORKER_method '''RAREMETALWORKER METHOD'''].
 
Method description and key formulae can be found in [http://genome.sph.umich.edu/wiki/RAREMETALWORKER_method '''RAREMETALWORKER METHOD'''].
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==For Binary Traits==
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RAREMETALWORKER currently treat all traits as quantitative. If your trait is binary, the odds ratio can be approximated from effect size estimates generated by RAREMETALWORKER. The installation/source package has a script included to augment the odds ratio estimates to the last column of the RAREMETALWORKER output. For details, please refer to [[RAREMETAL_DOWNLOAD_%26_BUILD#Calculating_Odds_Ratio_from_RAREMETALWORKER_output | '''Calculate Odds Ratio from RAREMETALWORKER output''']].
    
== Software Specifications ==
 
== Software Specifications ==
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For detailed description of command options, please go to [[RAREMETALWORKER_command_reference | '''command reference''']].
 
For detailed description of command options, please go to [[RAREMETALWORKER_command_reference | '''command reference''']].
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RAREMETALWORKER 0.4.9 -- A Forerunner of RareMetal
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          (c) 2012-2014 Shuang Feng, Dajiang Liu, Goncalo Abecasis
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  Please go to "http://genome.sph.umich.edu/wiki/RAREMETALWORKER#Where_to_Download" for the latest version.
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  Options:
 
  Options:
 
       Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
 
       Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
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       Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
 
       Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
 
                     --maleLabel [1], --femaleLabel [2]
 
                     --maleLabel [1], --femaleLabel [2]
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             others : --cpu [1]
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             others : --cpu [1], --kinOnly,
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                    --geneMap [../data/refFlat_hg19.txt]
 
         PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
 
         PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
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* When PED file has genotypes saved, there is no need for a VCF file as input.
 
* When PED file has genotypes saved, there is no need for a VCF file as input.
 
* RMW takes PED/DAT file in Merlin format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
 
* RMW takes PED/DAT file in Merlin format. Please refer to [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html PED/DAT format description] for details.
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* PED file requires "dummy" parents to be included in the pedigree file. To check the integrity of your PED/DAT file, please use [http://www.sph.umich.edu/csg/abecasis/PedStats '''pedstats''']. To add dummy parents into the pedigree, please use the [[Media:Script.tgz | '''perl script''']].
 
* An example PED file is in the following:
 
* An example PED file is in the following:
 
     1 1 0 0 1 1.5 1 23 A A A A A A A A A A
 
     1 1 0 0 1 1.5 1 23 A A A A A A A A A A
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* If --zip option is used, then the following will be generated automatically:
 
* If --zip option is used, then the following will be generated automatically:
 
   prefix.traitName.singlevar.score.txt.gz
 
   prefix.traitName.singlevar.score.txt.gz
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  prefix.traitName.singlevar.score.txt.gz.tbi
 
   prefix.traitName.singlevar.cov.txt.gz
 
   prefix.traitName.singlevar.cov.txt.gz
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  prefix.traitName.singlevar.cov.txt.gz.tbi
 
   prefix.singlevar.log
 
   prefix.singlevar.log
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* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
 
* In the file with summary statistics named prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
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  LDL mean= -0.00, variance=  1.00, heritability= 34.30
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LDL mean= -0.00, variance=  1.00, heritability= 34.30  
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  CHR     POS     REF_ALLELE     ALT_ALLELE     INFORMATIVE_N   FOUNDER_AF     ALL_AF  INFORMATIVE_AC  HWE_PVALUE      STAT   ALT_ALLELE_EFFSIZE     PVALUE
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CHR       POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF   ALL_AF  INFORMATIVE_AC  HWE_PVALUE      STAT ALT_ALLELE_EFFSIZE       PVALUE
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   10   45410002       G       A       6103    0.0341589      0.0341589      410     0.165893       126.205 0.309798       4.03074e-10
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   10 45410002         G         A           6103    0.034159  0.034159            410   0.165893 126.2050            0.309798 4.030740e-10
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   19   45412079       G       A       6103    0.0368124      0.0368124      434     0.714645       -265.84 -0.587356       7.87851e-36
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   19 45412079         G         A           6103    0.036812  0.036812            434   0.714645 -265.8400          -0.587356 7.878510e-36
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   19   45414451       G       A       6103    0.444989       0.444989       5312    0.0759271      -26.1212       -0.00837122    0.640058
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   19 45414451         G         A           6103    0.444989 0.444989           5312    0.075927  -26.1212           -0.008371  6.400580e-01
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* pvalues from the above output are from the family-based single variant score test.
 
* pvalues from the above output are from the family-based single variant score test.
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* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
 
* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:
 
    
 
    
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  CHR   POS       VAR_POS_IN_WINDOW                             LD_MATRIX
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CHR     POS                           VAR_POS_IN_WINDOW                                                                 LD_MATRIX
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  1  762320    762320,865628,865665,878744,879381,1560000   0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,
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  1 762320   762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,
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  1   865628     865628,865665,878744,879381,1560000,1864659   0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
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  1 865628 865628,865665,878744,879381,1560000,1864659           0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
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  1   878744     878744,879381,1560000,1864659,1877659         0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
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  1 878744       878744,879381,1560000,1864659,1877659             0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
    
=====Genomic Relationship Matrix (GRM)=====
 
=====Genomic Relationship Matrix (GRM)=====
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   [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial''']
 
   [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL and RAREMETALWORKER Tutorial''']
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== Change Log ==
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* Version 0.0.1 was released on 11/13/2012.
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* Modified Rare-Metal-Worker to let it output LD matrix by a sliding window. (11/14/2012)
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* Uploaded to public wiki. (11/16/2012)
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* Enabled writing log file by defalut. (11/18/2012)
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* 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)
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* Added HWE pvalue and call rate in summary statistics output. (11/27/2012)
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* Bugs fixed to solve compiling errors on some machines (Thank you Mary Kate!). Version 0.0.2 released. (11/30/2012)
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* Updated output format. Version 0.0.3 released. (12/3/2012)
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* More messages coded into log file. (12/4/2012)
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* Version 0.0.4 released. (12/5/2012)
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* Bug fixed for empirical kinship calculation when genotypes are read from VCF file. Version 0.0.5 released. (12/6/2012)
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* Version 0.0.6 released. (12/6/2012)
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* Updated output format for monomorphic sites. (12/7/2012)
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* Changed executable name into bin/raremetalworker. Version 0.0.7 released. (12/10/2012)
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* Fixed a bug when reading vcf file with ref or alt allele is missing. (2/5/2013)
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* Fixed a bug when there is missing genotype from VCF file. (2/2013)
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* Fixed a bug when handling chromosome X. Added sex labels option. (3/2/2013)
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* Optimized code to speed up the process of calculating empirical kinship. (3/3/2013)
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* Updated code to report allele frequencies calculated only from selected samples. (3/3/2013)
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* 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)
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* Added support for analyzing dosages from VCF in version 2.9. (8/27/2013)
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* Fixed the bug which causes crash when writing PDF when all variants are monomorphic. (10/6/2013)
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* Fixed a few bugs handling chromosome X. Generated warning messages when male genotypes are coded wrong in VCF file. (11/25/2013)
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* Released version 0.3.6 and fixed a minor bug that caused by code upgrades from version 0.3.5. (12/4/2013)
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* Released version 0.3.7. Added dominant and recessive models as options. The default model is additive. (1/7/2014)
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* Released version 0.4.0. Added phone home function. Saved Recessive and dominant results in separate files.
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* Released version 0.4.1. Fixed a bug handling variants in nonPAR region on chromosome X when all samples are male.
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* 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)
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* 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.
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* Released version 0.4.4. Fixed hwe=0.0 issue for monomorphic sites. (3/17/2014)
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* Released version 0.4.5. Fixed a bug when generating plots for recessive results. (3/18/2014)
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* Released version 0.4.6 binary. Fixed a bug in recessive and dominant results. (4/1/2014)
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* 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)
 
Abought
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