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Overlapping positions

Hi

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

rfuentes

Tagged:

• Hi @rfuentes . I'm a user like you. HaplotypeCaller merges SNPs and indels, but UnifiedGenotyper doesn't. Your variants at postions 10221399 (indel) and 10221400 (SNP) are different. Wouldn't leaving one of them out be like filtering your calls randomly?

chr02 10221399 . C .
chr02 10221399 . CA CCTA,C
chr02 10221400 . A C,T

UG was the standard fo long time, and some people have not yet updated their pipeline, it's understandable. We do not provide recommendations for choosing in mixed cases since it can depend on project objectives. But perhaps @tommycarstensen can share his experiences... 