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PGT and PID in VCF

Dear all,

I have been using a relatively recent nightly build of GATK to deal with some previous bug fix, and I now see some odd things in my VCF format, after using genotypegVCF.
Precisely some rows have this INFO field:

with these new PGT and PID which are present only some of the time. I have no idea what this means (and it also messes up my data processing). Does anyone know what these fields are about? And, unless they are very useful, how to get rid of them?

Thank you in advance,


Best Answer


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