We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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,
Brett

Best Answer

Answers

  • 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,
    Brett

Sign In or Register to comment.