Service notice: Several of our team members are on vacation so service will be slow through at least July 13th, possibly longer depending on how much backlog accumulates during that time. This means that for a while it may take us more time than usual to answer your questions. Thank you for your patience.

UnifiedGenotyper failure

I have twice run UnifiedGenotyper and the resultant .vcf file contains only part of chromosome 20. I do not see what I am doing wrong. Neither do the other two people in the lab who have extensive experience with GATKcat

Best Answer

Answers

  • Human error. I had a -L 20 argument in the command that I did not want, but somehow got in (cut and paste?). That is so human and makes me feel so stupid. But it is just the way we are built. We humans see what we expect.. This is exactly why GATK exists, it never overlooks anything it is set to detect. So sorry to bother you and thanks for the response.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hah, don't beat yourself up, it happens all the time :)
    I'm glad your problem is resolved.

Sign In or Register to comment.