Unified Genotyper

mjroy

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?

Geraldine_VdAuwera

Hi Megan, that is a very old version, so what you're seeing is probably due to a bug that we fixed a while back. I strongly recommend you update to a more recent version, at least post 2.0, and preferably the latest (we are currently on 2.3-9).

Geraldine_VdAuwera

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.

mjroy

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