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

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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

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