I am trying to convert my VCF files to plink format for some downstream processing in PLINK. Since VCF half calls are coded as
"0/.", "./1",... PLINK/1.9 raises an error flag for such calls in the
.ped file. What would be the easiest way to deal with such calls in the
I am aware that half calls can be circumvented from the
.map output using
--vcf-half-call argument, but is there a similar function for
If theres no way to correct half calls in the
.ped file, what would be the easiest way to recode half calls as missing calls in the VCF?