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Is it possible for GATK4 beta3 Mutect2 to output germline variants also?

By the default configuration, it seems that all variants are somatic. I could not find the parameter which would regulate that.


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Mutect2 is not a germline variant caller; its modeling algorithm is tuned specifically for somatic mutations. If you're looking for germline variation as well you'll need to use a germline caller like HaplotypeCaller in a separate run.

  • @Geraldine_VdAuwera,
    thanks for the fast reply. In the previous versions, correct me if I'm wrong, the output VCF contained both germline and somatic variants. Was that changed? Or maybe some parameter can prevent outputting of the germline variants. Here is the command line:
    java -Xmx2048M -jar /opt/gatk-package-4.beta.3-local.jar Mutect2 --output Tumor_exomeSeq.vcf --tumorSampleName Tumor_exomeSeq --reference Homo_sapiens.GRCh38.dna.primary_assembly.fa --input tumor_recalibrated.bam --input normal_recalibrated.bam --normalSampleName Normal_exomeSeq --intervals 9.bed --dbsnp dbsnp_144.hg38.vcf

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭


    I am not aware of previous versions of Mutect outputting germline variants.

    I am assuming you are asking about sites that are either in the PoN, germline resource or in the matched normal. For the sites in the PoN or germline resource, you can simply take a look at those in the resource files and compare them to the output of Mutect2. For the matched normal, it is best to run a germline variant caller like HaplotypeCaller. Note, FilterMutectCalls will also flag any sites called by Mutect2 that are in the PoN or germline resource or have a high LOD score in the normal.


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