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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!

How VQSR deals with multiallelic SNPs and Indel


May I know how VQSR deals with multiallelic SNPs and indels? How to classify them as pass or fail?


Best Answer


  • armarkesarmarkes LisbonMember

    Hi @Geraldine_VdAuwera

    Regarding this situation of multiallelic sites, I also have one question.
    I split multiallelic sites in my VCF using bcftools, but when I try to use GATK tool Variant Filtration, something happens when it finds repeated positions (first and second alternative allele) and stops reporting a bug.
    Do you know why this happen? How can I prevent this?

    Ana Rita

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Can you please post the vcf records involved and the error message?
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