We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Unified Genotyper quality call
I am running the unified genotyper in "EMIT_ALL_CONFIDENT_SITES" with the latest version of GATK and am getting some odd quality assignments of 10000030. It is clear that these sites are not very stellar, so I am wondering what is happening to these sites. Any thoughts?
Below is a snippet from one such region, starting with some seemingly "normal" rows and ending with this seemingly odd assessment of quality. Any thoughts? As some background info, this sample is quite different than reference, so not abnormal to have lots of missing regions when aligned against the reference that I used. It is bacterial. Here is the command line that I ran:
GenomeAnalysisTK.jar -T UnifiedGenotyper -dt NONE -I "$i" -R ../../Ref.fasta -baq RECALCULATE -nt 4 -ploidy 1 -out_mode EMIT_ALL_CONFIDENT_SITES -o "$j".vcf -stand_call_conf 100 -stand_emit_conf 100 -mbq 20 Ref 930 . C . 102 . AN=1;DP=2;MQ=150.00;MQ0=0 GT:DP:MLPSAC:MLPSAF 0:2 Ref 931 . C . 107 . AN=1;DP=2;MQ=150.00;MQ0=0 GT:DP:MLPSAC:MLPSAF 0:2 Ref 932 . T . 105 . AN=1;DP=2;MQ=150.00;MQ0=0 GT:DP:MLPSAC:MLPSAF 0:2 Ref 942 . A . 10000030 . DP=1;MQ=150.00;MQ0=0 GT . Ref 1109 . G . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1110 . A . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1111 . T . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1112 . T . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1113 . T . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1114 . A . 10000030 . DP=2;MQ=150.00;MQ0=0 GT . Ref 1115 . C . 10000030 . DP=2;MQ=150.00;MQ0=0 GT .