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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
GATK 3.3 UG question regarding DP in info and sample field.
We are trying to determine positions with low coverage using GATK 3.3 UnifiedGenotyper. Although there are walkers for this that may be more appropriate, the way the pipeline was originally set up in 2011 was to use the allbase vcf file and to pull DP. We have many clinically important genes with high homology and thus poor mapping quality reads. I was under the assumption that the DP in the FORMAT fields was filtered and thus would remove low MQ reads. However, this appears not to be the case and it looks like there is adequate good quality coverage at these positions (see below). Can you help clarify this?
14 23859426 . G . 241.23 . AN=2;DP=978;MQ=10.50;MQ0=904 GT:DP 0/0:978
14 23859427 . C . 241.23 . AN=2;DP=976;MQ=10.51;MQ0=902 GT:DP 0/0:976
14 23859428 . A . 238.23 . AN=2;DP=978;MQ=10.65;MQ0=902 GT:DP 0/0:978
14 23859429 . G . 241.23 . AN=2;DP=970;MQ=10.54;MQ0=896 GT:DP 0/0:970