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?

jh2663jh2663 NYCMember
edited April 25 in Ask the GATK team

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

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @jh2663

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

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @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.

Sign In or Register to comment.