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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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