The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.