How VQSR deals with multiallelic SNPs and Indel

Hi,

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

Tagged:

Best Answer

Answers

  • 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?

    Thanks
    Ana Rita

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Can you please post the vcf records involved and the error message?
Sign In or Register to comment.