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Can FilterMutectCalls filter by coverage?

JulsJuls Member ✭✭

Dear GATK team,

I could like to filter my mutect2 vcf file by coverage as well and thereby exclude high and low coverage regions like it is possible with VariantFiltration:

gatk VariantFiltration -R ref.fasta -V variants.vcf --filter-expression "!vc.hasAttribute('DP')" --filter-name "noCov" --filter-expression "vc.hasAttribute('DP') && DP < cutoffLow" --filter-name "lowCov" --filter-expression "vc.hasAttribute('DP') && DP > cutoffHigh" --filter-name "highCov" -O variants_filtered.vcf

Is this possible with FilterMutectCalls or can I use VariantFiltration on a mutect2 file as suggested above in addition to the regular filtering with FilterMutectCalls ?

Thank you so much!

Best Answer

  • bhanuGandhambhanuGandham Cambridge MA admin
    Accepted Answer

    Hi @Juls

    If you specifically want to filter for coverage then yes feel free to experiment with VariantFiltration. FilterMutectCalls does a lot of modeling and machine learning under the hood. If you absolutely must do coverage filtering, sure, use VariantFltration, but there's almost never a good reason not to rely solely on FilterMutectCalls. VariantFiltration can only do ad hoc hard filters.

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