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HaplotypeCaller Phasing "PID"

brcopelandbrcopeland New York, New York, USAMember
edited April 2015 in Ask the GATK team

I'm running into (what seems to me) an odd situation. I know that HaplotypeCaller will phase variants that occur closely together and my observation has previously been that the first such phased variant that occurs in a block is given a PID of the sort 12345_A_C, where 12345 is the genomic position along the current chromosome, the reference allele is A and the alternate allele is C. However, I observe in the first variant in a VCF a PID value of 69405_G_T, which would be fine if the first position in the VCF was in fact 69405. In this case though, the first position is 69428 - so the sample's call is phased with respect to a non-existent variant call?

Is there some reason why this would be intended behavior; or else I'll be happy to give more background info and data on this situation.

Thank you,

Best Answer


  • brcopelandbrcopeland New York, New York, USAMember

    Hi Geraldine,

    I actually thought of that shortly after posting my question but wasn't at a computer to edit. I haven't checked it but I think that is exactly right - the single sample was deemed potentially variant by HaplotypeCaller but then upon consideration of the rest of the cohort was considered most likely a false positive.

    Thanks again,

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