This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
[GATK 18.104.22.168] 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 22.214.171.124 to filter out calls with high SOR values.
But I can't find any filtering option to use this value with FilterMutectCalls in GATK 126.96.36.199 version. I only see the option --min-reads-per-strand. How can I filter out strand-biased calls in GATK 188.8.131.52 version?