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== Output Formats ==
== Output Formats ==
* There are two files generated automatically by default:
* There are three files generated automatically by default:
prefix.traitName.singlevar.score.txt
prefix.traitName.singlevar.score.txt
prefix.traitName.singlevar.cov.txt
prefix.traitName.singlevar.cov.txt
prefix.singlevar.log
* prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
* prefix.traitName.singlevar.score.txt contains summary statistics that are needed by Rare-Metal. An example is shown in below:
chr1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
chr1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
chr1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
chr1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,
* An example log file is in the following:
Summary statistics for trait LDL have been saved in LDL.singlevar.score.txt.
LD matrices for trait LDL have been saved in LDL.singlevar.cov.txt.
Rare-Metal-Worker handled all individuals as related.
The following parameters are in effect:
Input Files:
============================
--ped [APOE.ped]
--dat [APOE.dat]
--vcf []
Output Files:
============================
--prefix []
--LDwindow [1000000]
VC Options:
============================
--vcShared [false]
--vcX [false]
--useCovariates [false]
Trait Options:
============================
--makeResiduals [true]
--inverseNormal [true]
--traitName [LDL]
Kinship Source:
============================
--kinPedigree [true]
--kinGeno [false]
--kinFile []
--kinSave [false]
== Examples ==
== Examples ==
