Missing or Inconsistent call between single-sample and multi-sample SNP calling

meharmehar Member
edited February 13 in Ask the GATK team

Dear all,

I have generated a gVCF file using HaplotypeCaller (v3.7)and searched for a specific variant of interest which looks like below:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT    N417
 chr1   627033  .   C   <NON_REF>   .   .   END=627033  GT:DP:GQ:MIN_DP:PL  0/0:4:0:4:0,0,0

The same gVCF is used for genotype gVCF across multiple samples and the site looks like below (genotype is shown only for this sample):

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  N417
chr1    627033  .   C   T   101.69  .   AC=2;AF=0.011;AN=182;DP=500;ExcessHet=0.0127;FS=0.000;InbreedingCoeff=0.1696;MLEAC=2;MLEAF=0.011;MQ=51.17;QD=12.71;SOR=1.179    GT:AD:DP:GQ:PL  ./.:4,0:4

A bam out is generated which looks like below which supports an alternate allele "T".

The IGV or bamout result is supported by PCR. However, the call is not made by GATK. Could someone comment about this behaviour and best practices to rescue such variants?

Answers

  • meharmehar Member
    edited February 13

    And i have tried latest GATK version v4-0.1.2 and the result is the same

    KSN417A1
    ./.:4,0:4:.:0,0,0
    

    Could someone comment on this.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @mehar
    Hi,

    Notice the PLs are all 0 for the site. That is why the final VCF outputs ./. There is not enough confidence in any genotype.

    Can you color the reads in the bamout by sample? Please also post the original BAM file.

    Thanks,
    Sheila

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