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[[Category:RAREMETALWORKER]]
'''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'''].
'''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'''].
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.
If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] (goncalo at umich dot edu).
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL FAQ | '''FAQ''']]
* The [[RAREMETAL_Change_Log | '''Change Log''']]
== Key Features ==
== Key Features ==
==For Binary Traits==
==For Binary Traits==
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 ==
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
* '''Markers in PED and DAT file must be sorted by chromosome and position.'''
* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file.
* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWORKER#Example_Command_Lines | Example Command Lines]] for examples and [[RAREMETALWORKER_command_reference#Trait_Options | Trait Options]] for more information.
==== VCF File ====
==== VCF File ====
* 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
prefix.traitName.singlevar.score.txt.gz.tbi
prefix.traitName.singlevar.cov.txt.gz
prefix.traitName.singlevar.cov.txt.gz
prefix.traitName.singlevar.cov.txt.gz.tbi
prefix.singlevar.log
prefix.singlevar.log
* 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:
LDL mean= -0.00, variance= 1.00, heritability= 34.30
CHR POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF ALL_AF INFORMATIVE_AC HWE_PVALUE STAT ALT_ALLELE_EFFSIZE PVALUE
10 45410002 G A 6103 0.0341589 0.0341589 410 0.165893 126.205 0.309798 4.03074e-10
10 45410002 G A 6103 0.034159 0.034159 410 0.165893 126.2050 0.309798 4.030740e-10
19 45412079 G A 6103 0.0368124 0.0368124 434 0.714645 -265.84 -0.587356 7.87851e-36
19 45412079 G A 6103 0.036812 0.036812 434 0.714645 -265.8400 -0.587356 7.878510e-36
19 45414451 G A 6103 0.444989 0.444989 5312 0.0759271 -26.1212 -0.00837122 0.640058
19 45414451 G A 6103 0.444989 0.444989 5312 0.075927 -26.1212 -0.008371 6.400580e-01
* 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.
* 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:
CHR POS VAR_POS_IN_WINDOW LD_MATRIX
1 762320 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,
1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
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)=====
