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* The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
* The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
* there are ~1000 markers included in the VCF file.
* there are ~1000 markers included in the VCF file.
* To analyze this sample accounting for hidden relatedness, an empirical kinship should be calculated.
* To analyze this sample accounting for sample relatedness, an empirical kinship should be calculated.
* Go to $yourPath/bin/ and execute the following command:
* Go to $yourPath/bin/ and execute the following command:
cd raremetalworker/inputfiles
$yourpathforRAREMETALWORKER/bin/raremetalworker --ped example1.ped --dat example1.dat --vcf example1.vcf.gz
--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix ../yourprefix.example1
* The command above allows you to estimate relatedness according to common variants genotypes with good variant calling quality, adjust for covariates, quantile normalize the residuals before further association analysis of trait QT1. The following output are generated:
raremetalworker/yourprefix.example1.QT1.singlevar.score.txt (##includes association results, QC statistics, Genomic control, etc.)
raremetalworker/yourprefix.example1.QT1.singlevar.cov.txt (##includes covariance matrices of score statistics)
raremetalworker/yourprefix.example1.plots.pdf (##includes QQ plots and manhattan plots)
raremetalworker/yourprefix.example1.Empirical.Kinship.gz (##contains empirical kinship of all individuals who have at least one site genotyped.)
* Following the same strategy, example2 can also be analyzed using a similar command:
$yourpathforRAREMETALWORKER/bin/raremetalworker --ped example2.ped --dat example2.dat --vcf example2.vcf.gz
--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2
===Example 2===
===Example 2===
