chrX in plink to compatible regenie 2.0

[shihch...@gmail.com]

Hi Chris, 

I am trying to use Regenie 2.0 for GWAS analysis. One thing want to confirm with you. Regenie says we need to recode "male" to "female" so that male can be taken as diploid. However, I looks Plink1.9 already code male to "diploid", correct? 

To include X chromosome genotypes in step 1 and/or step 2, males should be coded as diploid so that their genotypes are 0/2. This can be done in PLINK by setting the sex of all individuals to female before generating the genotype file. 

Thanks. 

Shicheng

[Christopher Chang]

.bed and .pgen files use 0/2 to encode haploid genotypes.  So, if regenie completely ignores sex beyond inclusion as a covariate (I don't know whether this is the case), you're correct that there would be no need to set all sex values to female.