[GATK 4.1.2.0] FilterMutectCalls based on Strand Odds Ratio value?

jh2663

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

bhanuGandham

Hi @jh2663

Take a look at this tool, VariantFiltration, which you can use to filter for various annotations.

davidben

@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.