Hi there,
I have used haplotypecaller best practices to obtaine the vcf file. Next I used read backed phasing to phase my vcf file, however I am not able to properly understanding the results, e.g. below from 148004 to 148162, there are 5 SNPs and each SNP gives a HP '148004-1,148004-2'. I would highly appreciate if you let me know how to interpret this?
chr6 148004 . A C 97.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.196;ClippingRankSum=0.000;DP=22;ExcessHet=3.0103;FS=16.406;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=5.43;ReadPosRankSum=-0.850;SOR=3.227;VQSLOD=21.11;culprit=QD GT:AD:DP:GQ:HP:PL 0/1:14,4:18:99:148004-1,148004-2:126,0,546
chr6 148039 . T C 223.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.785;ClippingRankSum=0.000;DP=25;ExcessHet=3.0103;FS=29.863;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.66;ReadPosRankSum=-0.077;SOR=4.161;VQSLOD=22.85;culprit=MQRankSum GT:AD:DP:GQ:HP:PL:PQ 0/1:14,7:21:99:148004-1,148004-2:252,0,567:851.12
chr6 148040 . G A 223.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.000;ClippingRankSum=0.000;DP=25;ExcessHet=3.0103;FS=29.863;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.66;ReadPosRankSum=-0.038;SOR=4.161;VQSLOD=22.85;culprit=MQRankSum GT:AD:DP:GQ:HP:PL:PQ 0/1:14,7:21:99:148004-1,148004-2:252,0,567:993.02
chr6 148097 . G A 393.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.432;ClippingRankSum=0.000;DP=35;ExcessHet=3.0103;FS=13.249;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.58;ReadPosRankSum=0.148;SOR=0.749;VQSLOD=22.14;culprit=MQRankSum GT:AD:DP:GQ:HP:PL:PQ 0/1:12,15:27:99:148004-2,148004-1:422,0,251:881.95
chr6 148162 . G A 346.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.248;ClippingRankSum=0.000;DP=30;ExcessHet=3.0103;FS=3.682;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.87;ReadPosRankSum=-0.816;SOR=1.609;VQSLOD=22.25;culprit=MQRankSum GT:AD:DP:GQ:HP:PL:PQ 0/1:12,13:25:99:148004-1,148004-2:375,0,286:684.27
Thanks
Gaurav