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ERROR: GTs cannot be missing for some samples if they are available for others in the record

Hi:

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?

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