Hi,
I am following the best practice pipeline with version 3.6 of gatk and in order to reduce the amount of compound heteozygote variants found in my analysis, I recently chose to "mature" into using the phased gt annotations PID and PGT and I have very nice results.
However I found a high amount of variants with a dot ('.') in both fields in the vcfs I started to use the new analysis on.
I scanned around in the forums and documentation, however I could not find any sign what that means.
this is especially interesting, as I have several variants where the variants are on the same read only, however only a few of the variants are phased, the others show the '.'
I am pleased the with the outcome already however I fear that I might miss information.
I included the screenshot as well as an overview of the variants in that region.
I would appreciate it if you could shed some light on this issue, even if it is just " the dot means we were not sure about it"
chr1 152280671 . A C 3783.47 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.019;AN=2;BaseQRankSum=5.09;ClippingRankSum=0;DP=26522;ExcessHet=10.4471;FS=22.852;InbreedingCoeff=-0.0643;MLEAC=7;MLEAF=0.019;MQ=58.86;MQRankSum=-7.267;QD=1.96;ReadPosRankSum=-1.448;SOR=2.749;VQSLOD=-14.1;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:277,34:311:99:0|1:152280669_T_C:585,0,11704
chr1 152280685 . C A 9358.84 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.019;AN=2;BaseQRankSum=4.79;ClippingRankSum=0;DP=35550;ExcessHet=33.4707;FS=9.592;InbreedingCoeff=-0.1314;MLEAC=11;MLEAF=0.03;MQ=58.82;MQRankSum=-7.86;QD=3.99;ReadPosRankSum=-2.019;SOR=1.604;VQSLOD=-8.457;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:299,66:365:99:0|1:152280669_T_C:1871,0,12440
chr1 152280687 . C T 9105.01 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.019;AN=2;BaseQRankSum=5.67;ClippingRankSum=0;DP=35912;ExcessHet=38.6724;FS=9.592;InbreedingCoeff=-0.1438;MLEAC=12;MLEAF=0.033;MQ=58.81;MQRankSum=-7.86;QD=3.89;ReadPosRankSum=-1.766;SOR=1.605;VQSLOD=-8.451;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:299,66:365:99:0|1:152280669_T_C:1840,0,13062
chr1 152280688 . A G 9486.72 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.019;AN=2;BaseQRankSum=9.54;ClippingRankSum=0;DP=36233;ExcessHet=39.4426;FS=9.592;InbreedingCoeff=-0.1455;MLEAC=8;MLEAF=0.022;MQ=58.83;MQRankSum=-7.765;QD=4.02;ReadPosRankSum=-1.182;SOR=1.63;VQSLOD=-8.617;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:303,66:371:99:.:.:1926,0,13029
chr1 152280691 . A T 11612.7 VQSRTrancheSNP99.90to100.00 AC=1;AF=0.025;AN=2;BaseQRankSum=6.18;ClippingRankSum=0;DP=38167;ExcessHet=38.2356;FS=4.867;InbreedingCoeff=-0.1452;MLEAC=13;MLEAF=0.036;MQ=58.89;MQRankSum=-10.18;QD=3.99;ReadPosRankSum=-1.247;SOR=1.173;VQSLOD=-9.026;culprit=MQRankSum GT:AD:DP:GQ:PGT:PID:PL 0/1:281,110:391:99:.:.:3611,0,11146
