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Can you use Mutect2 with non-human samples?

kmmahankmmahan Member
edited October 2018 in Ask the GATK team

I want to use Mutect2 to subtract out variants present in a wild-type sample from variants present in an organism displaying a desired phenotype. Is Mutect2 appropriate for this? Can I use my wild-type .bam as the normal and the mutant phenotype .bam as the tumor? Do I need to create a PoN for this case? I only have two wild-type .bams

Best Answer


  • kmmahankmmahan Member

    I ran Mutect2 and created a PoN with non-phenotype genomes (normal) and many of the variants identified in the phenotype genome (tumor) are also present in the non-phenotype genome. This doesn't subtract variants from the normal genome?

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @kmmahan

    By default, the tool does not reassemble nor emit variant sites that match identically to a PoN variant, unless you enable genotyping of PoN sites using the --genotype-pon-sites option.

    Can you please share the exact command you used for somatic variant calling. Also please post the vcf records of the variant in the PoN that is showing up in the variants identified in the phenotype genome.


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