Complete this survey about your research needs and be entered to win an Amazon gift card or FireCloud credit.
Read more about it here!
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.6 is out. See the GATK4 beta page for download and details.

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?

Best Answer

Answers

Sign In or Register to comment.