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What variants does Mutect2 --germline-resource filter out?

Simoner92Simoner92 University of FlorenceMember
Hi everybody,

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 (af-only-gnomad.raw.sites.hg19.vcf).
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?

Thank you,


  • Tiffany_at_BroadTiffany_at_Broad Cambridge, MAMember, Administrator, Broadie, Moderator admin

    Hi @Simoner92 ,

    To clarify - Mutect2 is doing some prefiltering. FilterMutectCalls is the tool that will actually do the filtering. @davidben said that what is likely happening is that these variants with higher AFs are nearby ones with low AF's (within 100-200 bp) and they are getting called by Mutect2 because of this. It has to do with the assembly. Not to worry though, variants with higher AF's will get filtered out in the FilterMutectCalls step. Hope this helps!

  • Simoner92Simoner92 University of FlorenceMember
    Hi Tiffany,

    Thank you for your reply, it has been useful to understand the way Mutect2 call variants.

    Thank you
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