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