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  • GATK4 (4.1.2.0) Mutect2 --germline-resource option

    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,
    Simone

  • #2
    where did you get your germline resouce for hg19?

    Hi

    I am trying to download the germline resource for hg19 to run Mutect2. Would you please tell me where I can download it ?

    Thank you very much!

    Best,
    Lucy

    Comment


    • #3
      Try with the following link :
      Google Cloud Platform lets you build, deploy, and scale applications, websites, and services on the same infrastructure as Google.

      Comment


      • #4
        Thank you

        Hi Simoner,

        Thank you for your reply!

        I should download the files "af-only-gnomad.raw.sites.vcf" and its idx file, is that correct?

        thanks,
        Lucy

        Comment


        • #5
          Yes, with this link you should download hg19 af-only-gnomad.raw.sites.vcf

          Comment

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