Changes

* 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:

* 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.score.txt (## association results, QC statistics, Genomic control, etc.)

  raremetalworker/yourprefix.example1.QT1.singlevar.cov.txt (##includes covariance matrices of score statistics)

  raremetalworker/yourprefix.example1.QT1.singlevar.cov.txt (## covariance matrices of score statistics)

  raremetalworker/yourprefix.example1.plots.pdf (##includes QQ plots and manhattan plots)

  raremetalworker/yourprefix.example1.plots.pdf (## QQ plots and manhattan plots)

  raremetalworker/yourprefix.example1.Empirical.Kinship.gz (##contains empirical kinship of all individuals who have at least one site genotyped.)

  raremetalworker/yourprefix.example1.Empirical.Kinship.gz (##contains empirical kinship of all individuals who have at least one site genotyped, with id on top row.)

* Following the same strategy, example2 can also be analyzed using a similar command:

* Following the same strategy, example2 can also be analyzed using a similar command: