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 188.8.131.52] 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 184.108.40.206 to filter out calls with high SOR values.
But I can't find any filtering option to use this value with FilterMutectCalls in GATK 220.127.116.11 version. I only see the option --min-reads-per-strand. How can I filter out strand-biased calls in GATK 18.104.22.168 version?