Hi there,
gVCF files dont have FS or SOR in Info column.
X 32503194 . T C, 4947.77 . BaseQRankSum=1.490;ClippingRankSum=-0.791;DP=340;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.290;RAW_MQ=1665861.00;ReadPosRankSum=-1.449 GT:AD:DP:GQ:PL:SB 0/1:174,165,0:339:99:4976,0,5155,5497,5650,11147:90,84,76,89
When i convert gVCF to VCF using GenotypeGVCF, there is FS and SOR.. how is it calculated. What information from gVCF file is used in this calculation ?
X 32503194 . T C 4947.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.49;ClippingRankSum=-7.910e-01;DP=340;ExcessHet=3.0103;FS=4.835;MLEAC=1;MLEAF=0.500;MQ=70.00;MQRankSum=0.290;QD=14.60;ReadPosRankSum=-1.449e+00;SOR=0.806 GT:AD:DP:GQ:PL 0/1:174,165:339:99:4976,0,5155
Swati