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Can FilterMutectCalls filter by coverage?
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
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
Thank you so much!