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Error : Duplicate allele added to VariantContext

StevenSteven ParisMember


I download GnomAD vcf files in GRCh38 (hg19 remap). I want to convert this vcf in a table so i try to use VariantsToTable.
But i have this error :
The provided VCF file is malformed at approximately line number 10609: Duplicate allele added to VariantContext: C

line 10609 :
10 3101451 rs4881080 C C,T,G 191085017.71 PASS AC=237624,66,1;AF=9.99663e-01,2.77656e-04,4.20691e-06

I agree C is in REF and ALT colum but we can use VariantsToTable without check the integrity of vcf files?




  • SheilaSheila Broad InstituteMember, Broadie admin

    I guess not :smile: The GATK tools are usually pretty stringent with checks. Did you use LiftoverVCF to convert the hg38 VCFs to hg19? You may find this thread helpful as well.

  • Hi @Sheila!
    I'm having the same problem as you said, used crossMap to liftover Gnomad database GRCh37 to GRCh38. The link you posted leads to another thread with link which leads to another thread which ends without solution. Gnomad database is suggested for running Mutect2 workflow according to Broads best practice. Can you maybe instead solving this issue recommend some other resource database for Mutect2 with GRCh38 reference?

  • SheilaSheila Broad InstituteMember, Broadie admin
    edited September 2018


    I think you can use the Axiom resource file we provide (as it has the AF annotation) here.

    P.S. It seems an updated version of hg38 gnomad will be available sometime next year (or sooner).

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