ERROR: GTs cannot be missing for some samples if they are available for others in the record
I'm trying to work with exome chip data within gatk and so I've converted my ped / map files to vcf format using plink seq. I am getting the following error: When I run select variants in an attempt to pull out a few individual IDs, I get the error,
" GTs cannot be missing for some samples if they are available for others in the record".
I'm assuming this is referring to how some individuals may have "./." genotype vs. 0/0 0/1 or 1/1. Is there a way to work around this?