Hey GATK team,
I have a question regarding spanning deletions in one of my runs. Briefly, the study is set up so that we sequenced 21 pools of 3-5 animals each. Using GATK 3.5, I followed the Best Practices workflow as best as I could, but had to use hard filtering as this is a non-reference species. In my final variant call set, there are quite a few spanning deletions that don't seem to have supporting evidence for a "position of interest" within that deletion.
In other words, if I had a 5 bp spanning deletion at positions 1000 - 1005, I would expect there to be something else interesting (a SNP, whatever) to be somewhere between 1000 - 1005. Hopefully that is the correct understanding?
Here is an actual example:
chr9 62268141 . CACAGTGA C 46727.97 PASS AC=63;AF=0.354;AN=178;ANN=C|intron_variant|MODIFIER|COLEC10|ENSECAG00000018266|transcript|ENSECAT00000019417.1|protein_coding|1/5|c.148+4396_148+4402delACAGTGA||||||;BaseQRankSum=1.02;ClippingRankSum=0.00;DP=3820;FS=0.000;MLEAC=64;MLEAF=0.360;MQ=59.98;MQRankSum=0.350;QD=13.07;ReadPosRankSum=-4.150e-01;SOR=0.693;set=variant GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/1/1/1:104,56:160:17:2058,116,17,0,31,106,244,520,6247 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
chr9 62268143 . C * 44681.43 PASS AC=60;AF=0.337;AN=178;DP=3815;FS=0.000;MLEAC=63;MLEAF=0.354;QD=13.08;SOR=0.698;set=variant2 GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/0/0/0:158,0:158:0:0,0,0,0,0,0,0,0,582 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
chr9 62268144 . A * 46727.97 PASS AC=63;AF=0.354;AN=178;DP=3820;FS=0.000;MLEAC=64;MLEAF=0.360;QD=13.07;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/1/1/1:104,56:160:17:2058,116,17,0,31,106,244,520,6247 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
chr9 62268146 . T * 46727.97 PASS AC=63;AF=0.354;AN=178;DP=3820;FS=0.000;MLEAC=64;MLEAF=0.360;QD=13.07;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/1/1/1:104,56:160:17:2058,116,17,0,31,106,244,520,6247 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
chr9 62268147 . G * 46727.97 PASS AC=63;AF=0.354;AN=178;DP=3820;FS=0.000;MLEAC=64;MLEAF=0.360;QD=13.07;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/1/1/1:104,56:160:17:2058,116,17,0,31,106,244,520,6247 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
chr9 62268148 . A * 46727.97 PASS AC=63;AF=0.354;AN=178;DP=3820;FS=0.000;MLEAC=64;MLEAF=0.360;QD=13.07;SOR=0.693;set=variant2 GT:AD:DP:GQ:PL 0/0/0/0/0/0/0/1/1/1:166,61:227:11:2069,110,11,0,35,107,219,385,642,1110,9818 0/0/1/1/1/1/1/1/1/1:26,136:162:8:5756,1060,664,439,286,175,92,33,0,8,955 0/0/0/0/0/0/0/1:156,25:181:29:809,0,29,108,228,398,653,1105,8990 0/0/0/0/1/1/1/1:109,107:216:28:4085,380,131,28,0,32,139,395,5412 0/0/0/0/0/0/1/1/1/1:110,81:191:9:1550,287,104,27,0,9,52,135,282,572,5275 0/0/0/0/1/1/1/1/1/1:65,93:158:11:3620,495,248,122,49,11,0,19,79,227,3984 0/0/0/0/1/1/1/1:69,63:132:12:2358,212,69,12,0,25,96,261,3633 0/0/0/0/0/0/0/1:195,13:208:91:347,0,91,222,395,626,959,1537,11748 0/0/0/0/0/1/1/1:132,76:208:29:2746,170,29,0,33,124,296,642,6407 0/0/0/0/0/1:205,23:228:99:654,0,129,345,677,1271,11880 0/0/0/0/0/0/0/0:135,0:135:23:0,23,50,82,120,170,241,361,1800 0/0/0/0/0/0/0/0/1/1:146,28:174:10:898,10,0,35,98,186,305,468,709,1134,8574 0/0/0/0/0/0/1/1:101,45:146:1:1608,68,0,1,42,125,267,540,4419 0/0/0/0/0/0/0/0/1/1:109,33:142:5:1129,44,0,5,36,91,170,284,456,767,6255 0/0/0/0/0/1/1/1:98,75:173:1:2856,215,55,0,1,51,164,408,4095 0/0/0/0/0/0/1/1:130,51:181:13:1826,67,0,13,74,187,375,732,8147 0/0/0/0/1/1/1/1:99,95:194:23:3644,332,112,23,0,31,130,364,5154 0/0/0/0/0/1/1/1:104,56:160:17:2058,116,17,0,31,106,244,520,6247 0/0/0/0/0/0/0/1:128,11:139:52:294,0,52,134,244,394,610,988,6434 0/0/1/1/1/1/1/1:61,176:237:32:7280,1038,549,288,127,32,0,66,2454 0/0/0/0/0/1/1/1:81,37:118:1:1322,58,1,0,32,97,211,429,3404
I cannot find any evidence - even in non-filtered variants - of another "position of interest" at this locus.
The one thing I have noticed is that it seems that the exact genotype isn't consistent for each sample through the region. For example, animal-1 may be 0/0/0/0/1/1/1/1 at pos'n 1001, 0/0/0/0/1/1/1/1 at pos'n 1002, 0/0/0/0/0/1/1/1 at pos'n 1003, 0/0/0/0/1/1/1/1 at pos'n 4, etc. I don't believe that the reported differences in genotype are accurate reflections of true differences in genotypes, but rather a reflection of the slight variability in number of supporting reads at the different positions, subsequently affecting the PL and thus the final genotype. Would something like that be enough to bring these up as spanning deletions?
Thanks for your time and continued help, and sorry for the wall of text.
Cheers,
Russ