Entering edit mode
3.4 years ago
obidobi
▴
30
Hi, y'all!
Beagle SNP imputation software seems to be stuck in some scaffolds. Let me paste a couple of examples:
Window 298 (scaffold17559:158294-158294)
or
Window 235 (scaffold9691:3472-3472) Study markers: 1 Burnin iteration 1: 0 seconds Burnin iteration 2: 0 seconds Burnin iteration 3: 0 seconds Burnin iteration 4: 0 seconds Burnin iteration 5: 0 seconds
As you may have noticed, the start and the stop positions of those scaffolds seem to be equal.
scaffold9691 3472 . T C 31.57 PASS . GT:AD:BQ:BRC6:CM:CP:CU:DP:DP4:GP:GQ:SS 0/0:10,1:33.7,nan:0,6,0,0,0,0:.:.:.:11:6,0,0,0:0,31,32:31:5 0/0:3,4:36.7,nan:1,2,0,0,0,0:.:.:.:7:3,0,0,0:0,24,26:24:5 0/0:4,2:39.3,nan:1,2,0,0,0,0:.:.:.:6:3,0,0,0:0,24,26:24:5 0/0:5,1:38.8,nan:1,4,0,0,0,0:.:.:.:6:5,0,0,0:0,26,28:26:5 0/0:19,4:36.7,nan:3,10,0,0,0,0:.:.:.:23:13,0,0,0:0,12,11:11:5 0/0:2,0:40,nan:0,1,0,0,0,0:.:.:.:2:1,0,0,0:0,32,34:32:5 0/0:23,1:35.1,nan:0,8,0,0,0,0:.:.:.:24:8,0,0,0:0,30,32:30:5 0/0:6,3:37.8,nan:2,4,0,0,0,0:.:.:.:9:6,0,0,0:0,16,17:16:5 0/0:4,1:38.3,nan:1,2,0,0,0,0:.:.:.:5:3,0,0,0:0,24,26:24:5 0/0:7,3:39.3,nan:3,3,0,0,0,0:.:.:.:10:6,0,0,0:0,3,2:2:5 0/0:9,1:39.3,nan:1,5,0,0,0,0:.:.:.:10:6,0,0,0:0,26,28:26:5 0/0:11,1:33.6,nan:0,7,0,0,0,0:.:.:.:12:7,0,0,0:0,30,32:30:5 1/1:8,4:39,nan:4,3,0,0,0,0:.:.:.:12:7,0,0,0:12,3,0:3:5 0/0:6,1:39.5,nan:0,4,0,0,0,0:.:.:.:7:4,0,0,0:0,31,33:31:5 0/0:11,2:37.6,nan:2,3,0,0,0,0:.:.:.:13:5,0,0,0:0,15,15:15:5 0/0:5,2:39,nan:2,2,0,0,0,0:.:.:.:7:4,0,0,0:0,13,13:13:5 0/0:26,0:38.4,nan:0,14,0,0,0,0:.:.:.:26:14,0,0,0:0,29,30:29:5 0/0:6,0:38,nan:0,1,0,0,0,0:.:.:.:6:1,0,0,0:0,32,34:32:5 0/0:3,4:38.5,nan:0,2,0,0,0,0:.:.:.:7:2,0,0,0:0,31,34:31:5 0/0:12,2:38,nan:1,0,0,0,0,0:.:.:.:15:1,0,0,0:0,20,20:20:5 0/0:2,2:35,nan:0,1,0,0,0,0:.:.:.:4:1,0,0,0:0,32,34:32:5 0/0:10,0:36,nan:0,5,0,0,0,0:.:.:.:10:5,0,0,0:0,31,33:31:5 0/0:1,0:39,nan:0,1,0,0,0,0:.:.:.:1:1,0,0,0:0,32,34:32:5 0/0:5,0:37,nan:0,5,0,0,0,0:.:.:.:5:5,0,0,0:0,31,33:31:5 0/0:4,5:35.7,nan:2,1,0,0,0,0:.:.:.:9:3,0,0,0:0,10,10:10:5 ./.:.:.:.:.:.:.:.:.:.:.:. 0/0:17,3:35.9,nan:3,12,0,0,0,0:.:.:.:20:15,0,0,0:0,14,13:13:5 0/0:1,1:41,nan:1,0,0,0,0,0:.:.:.:2:1,0,0,0:0,18,18:18:5 0/0:11,3:35.8,nan:3,5,0,0,0,0:.:.:.:14:8,0,0,0:0,7,6:6:5 0/0:1,2:40.3,nan:2,1,0,0,0,0:.:.:.:3:3,0,0,0:0,10,10:10:5 1/1:3,3:36.7,nan:3,0,0,0,0,0:3:CH:0:7:3,0,0,0:15,6,0:6:5 ./.:.:.:.:.:.:.:.:.:.:.:. 1/1:2,4:40.2,nan:4,1,0,0,0,0:4:CH:1:6:5,0,0,0:21,4,0:4:5 1/1:1,3:40,nan:3,1,0,0,0,0:.:.:.:4:4,0,0,0:6,2,0:2:5 0/0:5,0:39,nan:0,2,0,0,0,0:.:.:.:6:2,0,0,0:0,31,34:31:5 0/0:12,4:39.1,nan:4,8,0,0,0,0:.:.:.:16:12,0,0,0:0,3,1:1:5 0/0:4,3:36.8,nan:2,3,0,0,0,0:.:.:.:7:5,0,0,0:0,15,15:15:50/0:4,2:28,nan:2,0,0,0,0,0:.:.:.:6:2,0,0,0:0,5,2:2:5 0/0:6,2:35.3,nan:1,3,0,0,0,0:.:.:.:8:4,0,0,0:0,25,27:25:5 0/0:3,1:33,nan:1,1,0,0,0,0:.:.:.:4:2,0,0,0:0,22,24:22:5 0/0:2,0:38,nan:0,1,0,0,0,0:.:.:.:2:1,0,0,0:0,32,34:32:5 0/0:6,2:38.7,nan:2,1,0,0,0,0:.:.:.:8:3,0,0,0:0,10,10:10:5 0/0:2,1:35.5,nan:1,1,0,0,0,0:.:.:.:3:2,0,0,0:0,22,24:22:5 0/0:16,6:39.7,nan:2,1,0,0,0,0:.:.:.:22:3,0,0,0:0,10,10:10:5 1/1:1,5:39.2,nan:5,1,0,0,0,0:5:CH:1:6:6,0,0,0:37,7,0:7:5 0/0:5,2:37.6,nan:2,3,0,0,0,0:.:.:.:7:5,0,0,0:0,17,17:17:5 0/0:5,0:40,nan:0,1,0,0,0,0:.:.:.:5:1,0,0,0:0,32,34:32:5 0/0:7,0:37,nan:0,5,0,0,0,0:.:.:.:7:5,0,0,0:0,31,33:31:5 0/0:9,2:37.1,nan:2,6,0,0,0,0:.:.:.:11:8,0,0,0:0,18,18:18:5 0/0:7,2:39.4,nan:1,4,0,0,0,0:.:.:.:9:5,0,0,0:0,26,28:26:5 0/0:6,4:40,nan:2,2,0,0,0,0:.:.:.:10:4,0,0,0:0,13,13:13:5 0/0:2,1:39,nan:0,1,0,0,0,0:.:.:.:3:1,0,0,0:0,32,34:32:5 0/0:9,1:38.1,nan:1,8,0,0,0,0:.:.:.:10:9,0,0,0:0,27,29:27:5 0/0:12,7:36.3,nan:1,3,0,0,0,0:.:.:.:19:4,0,0,0:0,25,27:25:5 0/0:10,4:37,nan:0,7,0,0,0,0:.:.:.:14:7,0,0,0:0,30,32:30:5 0/0:7,3:35.8,nan:3,7,0,0,0,0:.:.:.:10:10,0,0,0:0,10,9:9:5 0/0:1,1:32.5,nan:1,1,0,0,0,0:.:.:.:2:2,0,0,0:0,22,24:22:5 0/0:10,1:38.7,nan:0,9,0,0,0,0:.:.:.:11:9,0,0,0:0,30,31:30:5
and scaffold9691 actually has a stop position at 209137 so why BEAGLE takes its start position also as a stop position? I simply removed those two positions and it worked well but I wonder whether there is a better solution or not. Thanks!
