Poor consensus quality at chr12_MATERNAL:54,203,389-54,203,897

[nhansen]

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Issue location in assembly (use format chromosome:start-end, e.g., chr13_MATERNAL:3740148-9625296)

chr12_MATERNAL:54203389-54203897

Description of the issue

Poor consensus quality due to high T/C region. Not sure why DeepVariant calls didn't clean this up, and Sniffles call is too imprecise to suggest a correction.

[jzook]

This was also picked up in looking at the DV calls, but the large ins is missing from HiFi and filtered in the ONT callsets. Could potentially manually select variants from duplex vcf to correct
chr12_MATERNAL 54203513 . T TTC 9.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:36:14,17:0.472222:7,6,0 chr12_MATERNAL 54203514 . C T 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:19:33:30,3:0.0909091:0,19,27 chr12_MATERNAL 54203515 . T C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:18:36:33,3:0.0833333:0,18,26 chr12_MATERNAL 54203521 . TC T 5.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:5:36:19,17:0.472222:3,0,18 chr12_MATERNAL 54203522 . C CT 8.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:4:19:1,18:0.947368:6,0,3 chr12_MATERNAL 54203554 . T C 16.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:35:13,22:0.628571:13,0,0 chr12_MATERNAL 54203556 . T C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:23:36:30,3:0.0833333:0,23,33 chr12_MATERNAL 54203559 . CT C 7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:6:36:7,29:0.805556:5,10,0 chr12_MATERNAL 54203560 . T TC 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:17:7:1,6:0.857143:0,18,22 chr12_MATERNAL 54203590 . C CT 25.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:17:34:1,31:0.911765:25,17,0 chr12_MATERNAL 54203614 . T TCTCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCCCTCTCCCTCTC 0.7 RefCall . GT:GQ:DP:AD:VAF:PL ./.:8:35:19,5:0.142857:0,11,9 chr12_MATERNAL 54203615 . C CT 16.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:9:32:15,17:0.53125:15,9,0 chr12_MATERNAL 54203621 . T C 1.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:6:35:13,15:0.428571:0,9,7 chr12_MATERNAL 54203625 . T TC 23.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:16:34:0,23:0.676471:23,16,0 chr12_MATERNAL 54203627 . A C 31.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:28:36:0,36:1:31,31,0 chr12_MATERNAL 54203650 . C CCT 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:17:36:28,6:0.166667:0,18,22 chr12_MATERNAL 54203656 . T C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:27:36:31,5:0.138889:0,27,34 chr12_MATERNAL 54203662 . T C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:21:36:32,4:0.111111:0,22,27 chr12_MATERNAL 54203670 . T C 0.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:14:32:27,3:0.09375:0,14,24 chr12_MATERNAL 54203676 . C T 0.3 RefCall . GT:GQ:DP:AD:VAF:PL ./.:12:36:30,6:0.166667:0,11,26 chr12_MATERNAL 54203680 . T TC 12.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:7:34:6,27:0.794118:11,7,0 chr12_MATERNAL 54203687 . CCT C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:18:36:19,13:0.361111:0,23,19 chr12_MATERNAL 54203689 . T TCTCC 2.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:3:22:4,15:0.681818:0,6,1 chr12_MATERNAL 54203699 . T TC 30.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:25:36:0,36:1:30,26,0 chr12_MATERNAL 54203736 . T C 8.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:3:34:21,13:0.382353:5,0,1 chr12_MATERNAL 54203742 . T C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:18:35:31,4:0.114286:0,19,23 chr12_MATERNAL 54203748 . C T 0.9 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:35:24,11:0.314286:0,7,11 chr12_MATERNAL 54203751 . CT C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:18:35:29,6:0.171429:0,19,25 chr12_MATERNAL 54203752 . T TC 1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:30:23,5:0.166667:0,5,21 chr12_MATERNAL 54203753 . CCTCT C 2.9 RefCall . GT:GQ:DP:AD:VAF:PL ./.:3:33:11,18:0.545455:0,8,0 chr12_MATERNAL 54203756 . CT C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:17:18:14,4:0.222222:0,17,25 chr12_MATERNAL 54203757 . T TC 0.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:15:13:3,8:0.615385:0,15,19 chr12_MATERNAL 54203767 . CT C 6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:36:7,29:0.805556:4,12,0 chr12_MATERNAL 54203768 . T TCCCTC 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:16:7:0,2:0.285714:0,19,18 chr12_MATERNAL 54203775 . T TCC 0.4 RefCall . GT:GQ:DP:AD:VAF:PL ./.:11:35:26,8:0.228571:0,12,14 chr12_MATERNAL 54203776 . CT C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:17:36:18,12:0.333333:0,18,23 chr12_MATERNAL 54203777 . T C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:16:18:14,4:0.222222:0,20,18 chr12_MATERNAL 54203778 . CT C 0.1 RefCall . GT:GQ:DP:AD:VAF:PL ./.:18:29:17,12:0.413793:0,18,26 chr12_MATERNAL 54203781 . T C 0.3 RefCall . GT:GQ:DP:AD:VAF:PL ./.:12:31:24,7:0.225806:0,15,13 chr12_MATERNAL 54203954 . GA G 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:48:37:30,7:0.189189:0,48,62