Dear GATK team
Now I am trying to run HaplotypeCaller to call SNPs on the realigned bam files from a poplar species, and use the genome of Populus trichocarpa as reference. The coverage of different individual is 65%-70%. Firstly, I run HaplotypeCaller from the version of 3.6-0. Some individuals were successfully, but others not. The process would stop in some position of the genome when running on these individuals. with the Error Message:code exception. So I try to use the Version 3.2 to call SNPs on these individuals, and all were successfully. But I found there are some differences when I checked the g.vcf files.
#
version 3.6
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
Chr01 1 . A . . END=1 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 2 . C . . END=3 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,42
Chr01 4 . C . . END=4 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,11
Chr01 5 . A . . END=5 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,32
Chr01 6 . A . . END=6 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,79
Chr01 7 . A . . END=11 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,31
Chr01 12 . A . . END=13 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,79
Chr01 14 . C . . END=14 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,31
Chr01 15 . C . . END=17 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,53
Chr01 18 . A . . END=18 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,52
Chr01 19 . A . . END=20 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69
Chr01 21 . C . . END=21 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,52
Chr01 22 . C . . END=24 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,74
Chr01 25 . A . . END=25 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,62
Chr01 26 . A . . END=27 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,89
Chr01 28 . C . . END=28 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,62
Chr01 29 . C . . END=29 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,74
Chr01 30 . C . . END=30 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,57
Chr01 31 . C . . END=34 GT:DP:GQ:MIN_DP:PL 0/0:2:3:2:0,3,45
Chr01 35 . C . . END=35 GT:DP:GQ:MIN_DP:PL 0/0:2:0:2:0,0,26
Chr01 36 . C . . END=44 GT:DP:GQ:MIN_DP:PL 0/0:2:3:2:0,3,45
Chr01 45 . T . . END=118 GT:DP:GQ:MIN_DP:PL 0/0:1:0:0:0,0,0
Chr01 119 . A . . END=119 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,27
Chr01 120 . T . . END=121 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 122 . A . . END=122 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,37
Chr01 123 . T . . END=125 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 126 . A . . END=127 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,37
Chr01 128 . A . . END=129 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,15
Chr01 130 . T . . END=130 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 131 . T . . END=131 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,15
Chr01 132 . C . . END=132 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,27
Chr01 133 . A . . END=134 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 135 . T . . END=137 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,15
Chr01 138 . A . . END=139 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,32
Chr01 140 . A . . END=142 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,15
Chr01 143 . T . . END=143 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0
Chr01 144 . A . . END=146 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,3,27
#
version 3.2
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
Chr01 1 . A . . END=5 GT:DP:GQ:MIN_DP:PL 0/0:1:3:1:0,0,0
Chr01 6 . A . . END=30 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,31
Chr01 31 . C . . END=243 GT:DP:GQ:MIN_DP:PL 0/0:1:0:0:0,0,0
Chr01 244 . G . . END=244 GT:DP:GQ:MIN_DP:PL 0/0:3:6:3:0,6,90
Chr01 245 . T . . END=245 GT:DP:GQ:MIN_DP:PL 0/0:3:0:3:0,0,0
Chr01 246 . C . . END=247 GT:DP:GQ:MIN_DP:PL 0/0:6:15:4:0,9,135
Chr01 248 . C . . END=248 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,152
Chr01 249 . C . . END=250 GT:DP:GQ:MIN_DP:PL 0/0:6:15:6:0,15,225
Chr01 251 . G . . END=254 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,0
Chr01 255 . C . . END=256 GT:DP:GQ:MIN_DP:PL 0/0:6:15:6:0,15,225
Chr01 257 . T . . END=257 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,192
Chr01 258 . T . . END=260 GT:DP:GQ:MIN_DP:PL 0/0:6:15:6:0,15,225
Chr01 261 . A . . END=262 GT:DP:GQ:MIN_DP:PL 0/0:6:0:6:0,0,182
Chr01 263 . A . . END=263 GT:DP:GQ:MIN_DP:PL 0/0:6:15:6:0,15,225
Chr01 264 . G . . END=265 GT:DP:GQ:MIN_DP:PL 0/0:6:2:6:0,0,197
Chr01 266 . G . . END=267 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,234
Chr01 268 . C . . END=268 GT:DP:GQ:MIN_DP:PL 0/0:5:0:5:0,0,157
Chr01 269 . A . . END=276 GT:DP:GQ:MIN_DP:PL 0/0:5:15:5:0,15,192
Chr01 277 . G T, 192.03 . DP=5;MLEAC=2,0;MLEAF=1.00,0.00;MQ=30.05;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,5,0:5:15:225,15,0,225,15,225:0,0,5,0
Chr01 278 . A . . END=294 GT:DP:GQ:MIN_DP:PL 0/0:6:18:5:0,15,219
Chr01 295 . A G, 236.90 . DP=6;MLEAC=2,0;MLEAF=1.00,0.00;MQ=31.93;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,6,0:6:18:270,18,0,270,18,270:0,0,6,0
Chr01 296 . A . . END=298 GT:DP:GQ:MIN_DP:PL 0/0:6:18:6:0,18,256
Chr01 299 . G . . END=305 GT:DP:GQ:MIN_DP:PL 0/0:7:21:7:0,21,312
Chr01 306 . T C, 326.80 . DP=8;MLEAC=2,0;MLEAF=1.00,0.00;MQ=34.12;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,8,0:8:24:360,24,0,360,24,360:0,0,8,0
Chr01 307 . G . . END=313 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,328
Chr01 314 . T A, 326.80 . DP=8;MLEAC=2,0;MLEAF=1.00,0.00;MQ=34.12;MQ0=0 GT:AD:DP:GQ:PL:SB 1/1:0,8,0:8:24:360,24,0,360,24,360:0,0,8,0
Chr01 315 . T . . END=315 GT:DP:GQ:MIN_DP:PL 0/0:8:8:8:0,9,287
Chr01 316 . C . . END=317 GT:DP:GQ:MIN_DP:PL 0/0:8:24:8:0,24,344
So I have two questions:
1, How can I deal with the ERROR of Coed Exception?
2, Could I join the g.vcf files from two versions together?(I tryed, and worked successfully)