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GATK HC joint call gives multiple lines for same variant

5581681555816815 TNMember
edited December 2016 in Ask the GATK team


I was doing some QC and happen to see the following behavior that are not what i wanted/expected:

chr4 151267927 . A C 43.77 PASS AC=50;AF=0.532;AN=94;DP=739 GT:AD:DP:GQ:PGT:PID:PL ...
chr4 151267927 . A AC,AAC 43.77 PASS AC=6,1;AF=0.429,0.071;AN=14;DP=97;MLEAC=1;MLEAF=0.500 ...
chr4 151267927 . A C,AC 426.77 PASS AC=105,4;AF=0.491,0.019;AN=214;DP=1815 GT:DP:GQ:PGT:PID

This would be fine until i perform variant selection, e.g. select SNP/INDEL will both missing the third line.

I am using GATK 3.4 (GenotypeGVCFs,Version=3.4-0-g7e26428)
The VCF is merged from 2000 samples, NOT joint genotyping.

Any way to fix this using GATK? hope i am not missing anything.



Best Answer


  • KurtKurt Member ✭✭✭

    I think the third line would be classifed as MIXED

  • 5581681555816815 TNMember

    @ Geraldine_VdAuwera @ Kurt thanks.
    Our automated pipeline is set up to perform bam->gvcf->vcf, however on individual sample level.
    It is planned to perform joint call using the gvcf files, but has not been done at this point.

    I had the issue because I need to look into one gene quickly, so i sliced the variant calls out and merged them.

    Yes indeed it is MIXED. I think I confused with bcftools which will report this "MIXED" line if I select snps or indels.

    Thanks a lot,


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Ah ok, that makes more sense, thanks for clarifying.

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