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Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Difference between dbsnp file in gatk3 and germline-resource file in gatk4 in Mutect2 analysis?

Dear all,
I have three questions.
1. What is difference between dbsnp file (e.g dbsnp_138.hg19.vcf) in gatk3 and germline-resource file (e.g af-only-gnomad.vcf.gz) in gatk4? How similar are they?

2. Are both of them as a blacklist in Mutect2 analysis?

3. What is rate of overlap between panel-of-normals file (e.g pon.vcf.gz) and dbsnp file (e.g dbsnp_138.hg19.vcf) or germline-resource (e.g af-only-gnomad.vcf.gz)?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited May 3

    Hi @mohamadzamani

    1) We do not recommend using dbsnp(as in gatk3) and hence in GATK4 we recommend using gnomad instead.
    2) gnomad is used to filter germline variants from somatic ones in the mutect2 analysis.
    3) panel of normals is used to filter out variants which maybe sequencing artifacts and gremline resource is used to filter out germline variants.

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