Heads up:
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.
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.
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!
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.
[GATK 4.1.2.0] FilterMutectCalls based on Strand Odds Ratio value?

Hi, I was able to get SOR values in the vcf file using Mutect2 --annotation StrandOddsRatio option in GATK 4.1.2.0 to filter out calls with high SOR values.
But I can't find any filtering option to use this value with FilterMutectCalls in GATK 4.1.2.0 version. I only see the option --min-reads-per-strand. How can I filter out strand-biased calls in GATK 4.1.2.0 version?
thanks
Answers
Hi @jh2663
Take a look at this tool, VariantFiltration, which you can use to filter for various annotations.
@jh2663
--min-reads-per-strand
is a nonstandard filter that we include for people who want an extra-stringent test of strand bias and don't mind losing sensitivity. Otherwise,FilterMutectCalls
learns a model of strand bias and filters automatically. You could filter based on SOR on top of that if you wish, but we have not tested this approach.