Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Quality value in Unified Genotyper, haploid option

I am attempting to produce consensus genome sequences from haploid Drosophila embryos sequenced to 30x coverage on the Illumina HiSeq, and when I use Unified Genotyper with the haploid (ploidy 1) option and EMIT_ALL_SITES, I get quality values of 3.01 for all sites that match the reference. Here are a few lines of my output vcf:

1 632 . A . 3.01 LowQual DP=250;DS;MQ=55.47;MQ0=0 GT .
1 633 . A . 3.01 LowQual DP=250;DS;MQ=55.49;MQ0=0 GT .
1 634 . G . 3.01 LowQual DP=250;DS;MQ=55.10;MQ0=0 GT .
1 635 . G . 3.01 LowQual DP=250;DS;MQ=55.48;MQ0=0 GT .
1 636 . A . 3.01 LowQual DP=250;DS;MQ=55.94;MQ0=0 GT .
1 637 . T C 735 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.939;DP=250;DS;Dels=0.00;FS=0.990;HaplotypeScore=90.4026;MLEAC=1;MLEAF=1.00;MQ=54.72;MQ0=0;MQRankSum=2.513;QD=2.94;ReadPosRankSum=0.118;SB=-4.345e-03 GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:126,123:250:99:1:1.00:765,0
1 638 . A . 3.01 LowQual DP=250;DS;MQ=54.09;MQ0=0 GT .
1 639 . T . 3.01 LowQual DP=250;DS;MQ=54.30;MQ0=0 GT .
1 640 . G . 3.01 LowQual DP=250;DS;MQ=54.50;MQ0=0 GT .
1 641 . A . 3.01 LowQual DP=250;DS;MQ=54.39;MQ0=0 GT .
1 642 . C . 3.01 LowQual DP=250;DS;MQ=53.83;MQ0=0 GT .

Since I am producing a consensus from the VCF output, I really need some quality value for all called sites, both variable and invariable. Is there any way to do this in GATK?

Answers

Sign In or Register to comment.