Unified Genotyper

mjroymjroy Posts: 2Member
edited February 2013 in Ask the GATK team

I am using Unified Genotyper to call variants from multiple samples. I have used the emit_all_confident_sites flag. The output vcf file occasionally has two entries for one position. It is always a monomorphic site and the depth between the two entries is quite different. Usually one entry has very high depth & when I return to the original bam file, the depth does not match. Any idea what I am missing here?

Post edited by Geraldine_VdAuwera on

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,423Administrator, GATK Developer admin

    Can you tell me what version you are using? Also, it would be helpful if you could post the lines from the VCF that you find problematic.

    Geraldine Van der Auwera, PhD

  • mjroymjroy Posts: 2Member

    I am using version 1.5. Here are a few lines of the vcf:

    chr1 10024 . C . 68.75 PASS AC=0;AF=0.00;AN=100;DP=29100;MQ=7.41;MQ0=23107 GT:DP 0/0:489 0/0:494 0/0:650 0/0:509 0/0:456 0/0:658 0/0:532 0/0:493 0/0:470 0/0:533 0/0:670 0/0:488 0/0:638 0/0:336 0/0:602 0/0:823 0/0:967 0/0:810 0/0:773 0/0:824 0/0:659 0/0:716 0/0:919 0/0:470 0/0:471 0/0:876 0/0:868 0/0:780 0/0:512 0/0:462 0/0:432 0/0:484 0/0:346 0/0:854 0/0:578 0/0:488 0/0:539 0/0:515 0/0:422 0/0:355 0/0:561 0/0:449 0/0:326 0/0:583 0/0:343 0/0:588 0/0:560 0/0:593 0/0:713 0/0:402 chr1 10024 . C . 46.19 LowQual AC=0;AF=0.00;AN=100;DP=30112;DS;MQ=7.41;MQ0=23973 GT:DP 0/0:36 0/0:33 0/0:44 0/0:29 0/0:32 0/0:37 0/0:29 0/0:33 0/0:26 0/0:24 0/0:25 0/0:19 0/0:42 0/0:31 0/0:29 0/0:47 0/0:64 0/0:64 0/0:36 0/0:41 0/0:22 0/0:29 0/0:46 0/0:12 0/0:36 0/0:33 0/0:40 0/0:31 0/0:27 0/0:23 0/0:17 0/0:32 0/0:21 0/0:25 0/0:57 0/0:27 0/0:38 0/0:38 0/0:20 0/0:29 0/0:29 0/0:28 0/0:11 0/0:35 0/0:31 0/0:46 0/0:26 0/0:44 0/0:39 0/0:30

    The same reference allele, noted twice, with two difference qualities and different depths.

    Let me know your thoughts, Megan

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