Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Haplotypecaller

Biorunner88Biorunner88 Member
edited December 2016 in Ask the GATK team

Hi I'm using the Haplotypecaller 3.4 in my pipeline, and I've detected this Issue. Depth is 37, with such a huge quality and when looking at the last column I see a GT 1/1 suported by an AD of 0,0 and a DO o 0.

Have you noticed this? If so, has this been corrected in 3.5?
It is giving me problems with other steps as depth is 0.

Thanks

chr11 10823576 . C CACACTCCTAAAATAGTTTCATGTTTTAATAGCAAATGAAATCACATATATTGCAGAATTTAACATTTGTTGCCTAA 5199.77 PASS DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,0:0:99:5180,332,0

Tagged:

Answers

  • I've checked this specific position with IGV and out of ~47 reads that align in this position 3 of them are A, the rest are C. The A change is happening at the beginning of the reads. The rest of the bases are ok, so there is no change of a C to the string of characters as stated by GATK. I'm going to run this same analysis using GATK3.5 to see whether this error disappears.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Biorunner88
    Hi,

    Have a look at this article.

    Can you try with the latest version (3.6) as well?

    Also, have you looked at the bamout file?

    -Sheila

Sign In or Register to comment.