I am new analyzing WES and I try GATK4 workflow for the detection of somatic variants.
I run Mutect2 in tumor-only mode with these commands:
gatk Mutect2 -R reference.ucsc.hg19.fasta -L Target.bed -I input.bam --f1r2-tar-gz input.tar.gz -O output1.unfiltered.vcf --germline-resource af-only-gnomad.raw.sites.hg19.vcf [max-population-af default value = 0.01] gatk Mutect2 -R reference.ucsc.hg19.fasta -L Target.bed -I input.bam --f1r2-tar-gz input.tar.gz -O output2.unfiltered.vcf [max-population-af default value = 0.01]
For the first command I obtained a vcf with around 40000 variants whereas with the second a vcf with around 100000 variants. I expected that
--germline-resource filters out germline variants based on AF in the resource (
However I notice that
output1.unfiltered.vcf contains variants with POPAF (negative log 10 population allele frequencies of alt alleles) values that correspond to AF (in the resource) more than 0.01.
Does anybody know the logic used by Mutect2 to filter out variants based on germline resource? Is possible that Mutect2 consider other parameters than AF in the resource?