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I'm wondering why some positions in VCF overlap. Can GATK skip emitting positions that are already part of an indel/concatenated ref?
We need to use EMIT_ALL_SITES but it's quite confusing if a position is represented multiple times especially if indel is present. I understand that there is always a duplicated position preceding an indel, but the positions after the indel should ideally be not overlapping the neighboring positions. Please see some examples below:
chr02 28792823 . C . 34.23 . AN=2;DP=12;MQ=57.31;MQ0=0 GT:DP 0/0:12
chr02 28792823 . CAA . 10000037.27 . AN=2;DP=12;MQ=57.31;MQ0=0 GT:AD:DP 0/0:12:12
chr02 28792824 . A . . . DP=12;MQ=57.31;MQ0=0 GT ./.
chr02 28792825 . A . 31.22 . AN=2;DP=12;MQ=57.31;MQ0=0 GT:DP 0/0:7
chr02 314879 . T . 100.23 . AN=2;DP=27;MQ=55.82;MQ0=0 GT:DP 0/0:27
chr02 314879 . TAGAG T,TAG 647.19 . AC=1,1;AF=0.500,0.500;AN=2;DP=27;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=55.82;MQ0=0;QD=23.97;RPA=8,6,7;RU=AG;STR GT:AD:DP:GQ:PL 1/2:0,9,11:26:99:989,445,424,395,0,335
chr02 314880 . A . 43.23 . AN=2;DP=26;MQ=55.66;MQ0=0 GT:DP 0/0:5
chr02 314881 . G . 40.23 . AN=2;DP=25;MQ=55.47;MQ0=0 GT:DP 0/0:4
chr02 314882 . A . 73.23 . AN=2;DP=25;MQ=55.47;MQ0=0 GT:DP 0/0:16
chr02 314883 . G . 73.23 . AN=2;DP=25;MQ=55.47;MQ0=0 GT:DP 0/0:16
This next example even calls a SNP for position 10221400 even if deletion occurs in 10221399.
chr02 10221399 . C . 76.23 . AN=2;DP=17;MQ=58.74;MQ0=0 GT:DP 0/0:17
chr02 10221399 . CA CCTA,C 143.19 . AC=1,1;AF=0.500,0.500;AN=2;DP=17;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.74;MQ0=0;QD=8.42 GT:AD:DP:GQ:PL 1/2:0,8,6:17:99:527,131,112,185,0,143
chr02 10221400 . A C,T 287.29 . AC=1,1;AF=0.500,0.500;AN=2;DP=17;Dels=0.29;FS=0.000;HaplotypeScore=6.7569;MLEAC=1,1;MLEAF=0.500,0.500;MQ=58.74;MQ0=0;QD=16.90 GT:AD:DP:GQ:PL 1/2:0,4,8:12:88:407,294,285,112,0,88
chr02 10221401 . A C 163.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DP=17;Dels=0.00;FS=1.913;HaplotypeScore=9.7562;MLEAC=1;MLEAF=0.500;MQ=58.74;MQ0=0;MQRankSum=1.558;QD=9.63;ReadPosRankSum=2.764 GT:AD:DP:GQ:PL 0/1:11,6:17:99:192,0,392
chr02 10221402 . A . 76.23 . AN=2;DP=17;MQ=58.74;MQ0=0 GT:DP 0/0:17
Thanks in advance for your help.