Recommended filters from Mutect2 Filtermutectcalls

[gevro]

Hi, In your current snakemake pipeline, the FILTER columns to remove from Mutect output (for example 'str_contraction' and 'multiallelic') are based on prior versions of Mutect. What FILTER values do you recommend to remove before input into MF from Mutect2 FilterMutectCalls?

base_qual clustered_events contamination fragment germline haplotype map_qual multiallelic orientation panel_of_normals position slippage strand_bias weak_evidence

Thanks.

[douym]

Hi, In your current snakemake pipeline, the FILTER columns to remove from Mutect output (for example 'str_contraction' and 'multiallelic') are based on prior versions of Mutect. What FILTER values do you recommend to remove before input into MF from Mutect2 FilterMutectCalls?

base_qual clustered_events contamination fragment germline haplotype map_qual multiallelic orientation panel_of_normals position slippage strand_bias weak_evidence

Thanks.

Hi @gevro ,

You could use multiallelic as the filter. The set of filters might not be so essential, since I've tried other callers (GATK, Strelka, MosaicHunter) with their default settings and still the precisions were high.

Best wishes,

Yanmei

[gevro]

Thank you.