Haplotype caller reports a variant when using the gVCF format but not when using the VCF format
Dear GATK team,
I have a variant that is called when setting the --emitRefConfidence to GVCF but it is not called when the output is switched to the VCF format.
chr11 108250864 . G C, 317.78 . BaseQRankSum=0.294;ClippingRankSum=0.000;DP=12;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQ=43200.00;ReadPosRankSum=-0.582 GT:AD:DP:GQ:PL:SB 0/1:1,11,0:12:0:343,0,0,346,33,378:0,1,5,6
chr11 108250864 . G C 317.78 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.294;ClippingRankSum=0.000;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=26.48;ReadPosRankSum=-0.582;SOR=0.293 GT ./.
Please, find attached an IGV screenshot of this region. The variant seems obvious.
Any help would be much appreciated.
Thanks very much in advance.