indel representation is wrong
ekg opened this issue · 2 comments
ekg commented
Found a "small"!! problem with the indel representation.
hhga -f ~/ref/hs37d5.fa -b 1:3675000-3676000.fn.vial1.bam -v lodz3.fn.clean.vcf.gz -r 1:3675803-3676000 -w 16 | sed s/\|/\\n\|/g | column | cut -f 1,9-14 -d\ | sed 's/ / ... /' | column -t
|ref ... 8T:1 9C:1 10M:1 11M:1 12M:1 13M:1
|hap1 ... 8M:1 9R:1 10M:1 11M:1 12M:1 13M:1
|hap2 ... 8M:1 9R:1 10AATTATTTAAA:1 11M:1 12M:1 13M:1
|geno1 ... 8M:1 9R:1 10M:1 11M:1 12M:1 13M:1
|geno2 ... 8M:1 9R:1 10AATTATTTAAA:1 11M:1 12M:1 13M:1
|aln0 ... 8R:32 9R:42 10A:42 11A:42 12T:42 13T:42
|aln1 ... 8R:37 9R:42 10A:42 11A:32 12T:32 13T:42
|aln2 ... 8R:42 9R:32 10A:32 11A:11 12T:32 13T:11
|aln3 ... 8R:42 9R:42 10A:42 11A:42 12T:42 13T:42
|aln4 ... 8R:42 9R:42 10A:42 11A:42 12T:37 13T:42
|aln5 ... 8R:42 9R:42 10A:42 11A:42 12T:42 13T:42
|aln6 ... 8R:42 9R:42 10A:42 11A:42 12T:37 13T:42
|aln7 ... 8R:42 9R:42 10A:42 11A:42 12T:42 13T:42
|aln8 ... 8R:42 9R:42 10A:42 11A:42 12T:42 13T:42
|aln9 ... 8R:32 9R:32 10M:1 11M:1 12M:1 13M:1
|aln10 ... 8R:37 9R:22 10M:1 11M:1 12M:1 13M:1
|aln11 ... 8R:37 9R:32 10M:1 11M:1 12M:1 13M:1
|aln12 ... 8R:27 9R:42 10M:1 11M:1 12M:1 13M:1
|aln13 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln14 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln15 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln16 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln17 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln18 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln19 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln20 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln21 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln22 ... 8R:37 9R:32 10M:1 11M:1 12M:1 13M:1
|aln23 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln24 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln25 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln26 ... 8R:37 9R:27 10M:1 11M:1 12M:1 13M:1
|aln27 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln28 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln29 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln30 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln31 ... 8R:32 9R:27 10M:1 11M:1 12M:1 13M:1
|aln32 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln33 ... 8R:42 9R:42 10M:1 11M:1 12M:1 13M:1
|aln34 ... 8R:42 9R:27 10M:1 11M:1 12M:1 13M:1
|aln35 ... 8M:1 9M:1 10M:1 11M:1 12M:1 13M:1
|aln36 ... 8M:1 9R:32 10M:1 11M:1 12M:1 13M:1
|aln37 ... 8M:1 9R:11 10M:1 11M:1 12M:1 13M:1
ekg commented
Before:
1_3675803_C_CAATTATTTAAA
reference CACAAATTC
hap .........
hap .........
geno .........
geno .........
SodqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2202:9749:37753
SodqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2216:7110:46578
SodqfXYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2224:2969:63842
sOdqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2204:8348:36417
sOdqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1211:11891:17236
SodqfXYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:5943:15232
SodqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2111:32475:3032
SodqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:23553:44644
SodqFxYPZI .........AATTATT 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1204:18366:71700
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2110:10439:38315
sOdqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2108:32211:52327
SodqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1211:15839:43273
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2123:29237:25728
SodqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2221:21645:44644
SodqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:6531:41462
sOdqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2209:10226:33692
sOdqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1211:17757:2575
sOdqfXYPZI A........ 0.9 0.9 60 ST-E00185:49:H5LVWCCXX:5:2109:3801:2346
SOdqFxYPZi ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1201:26466:51553
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2222:32231:48213
SODqFxyPZi ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2201:26131:48934
SoDqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2108:13413:29191
SoDqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1108:12215:30105
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1108:12226:30088
SodqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1205:3131:5651
sOdqfXYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1106:12205:20840
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1219:3913:29156
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1102:26963:17500
SoDqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1108:29521:38421
sOdqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:1218:3009:65776
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2217:28851:9800
SodqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2106:5334:14283
sOdqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2113:11738:53645
sODqFxYPZI ......... 1.0 1.0 60 ST-E00185:49:H5LVWCCXX:5:2113:11353:54032
SodqfXYPZI ........ 0.9 0.9 60 ST-E00185:49:H5LVWCCXX:5:2122:18752:23038
sOdqFxYPZI ... 0.3 0.3 60 ST-E00185:49:H5LVWCCXX:5:1121:14601:36452
sOdqFxYPZI . 0.1 0.1 60 ST-E00185:49:H5LVWCCXX:5:2122:5719:41814
sOdqfXYPZI . 0.1 0.1 60 ST-E00185:49:H5LVWCCXX:5:2221:19442:38087
QUAL:8672.0
Fixed:
1_3675803_C_CAATTATTTAAA
reference CACAAATTC-------
hap .........-------
hap .........AATTATT
geno .........-------
geno .........AATTATT
SodqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1211:15839:43273
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2123:29237:25728
SodqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2221:21645:44644
SodqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2115:6531:41462
sOdqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2209:10226:33692
sOdqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1211:17757:2575
SodqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2202:9749:37753
SodqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2216:7110:46578
sOdqfXYPZI A........------- 0.9 0.5 60 ST-E00185:49:H5LVWCCXX:5:2109:3801:2346
SOdqFxYPZi .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1201:26466:51553
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2222:32231:48213
SODqFxyPZi .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2201:26131:48934
SoDqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2108:13413:29191
SoDqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1108:12215:30105
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1108:12226:30088
SodqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1205:3131:5651
SodqfXYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2224:2969:63842
sOdqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2204:8348:36417
sOdqfXYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1106:12205:20840
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1219:3913:29156
sOdqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:1211:11891:17236
SodqfXYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:5943:15232
SodqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2111:32475:3032
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1102:26963:17500
SoDqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1108:29521:38421
sOdqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:1218:3009:65776
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2106:5334:14283
SodqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2217:28851:9800
SodqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:23553:44644
sOdqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2113:11738:53645
sODqFxYPZI .........------- 1.0 0.6 60 ST-E00185:49:H5LVWCCXX:5:2113:11353:54032
SodqFxYPZI .........AATTATT 0.6 1.0 60 ST-E00185:49:H5LVWCCXX:5:1204:18366:71700
SodqfXYPZI ........------- 0.9 0.5 60 ST-E00185:49:H5LVWCCXX:5:2122:18752:23038
SodqFxYPZI ......... 0.6 0.6 60 ST-E00185:49:H5LVWCCXX:5:2110:10439:38315
sOdqFxYPZI ......... 0.6 0.6 60 ST-E00185:49:H5LVWCCXX:5:2108:32211:52327
sOdqFxYPZI .------- 0.5 0.1 60 ST-E00185:49:H5LVWCCXX:5:2122:5719:41814
sOdqfXYPZI .------- 0.5 0.1 60 ST-E00185:49:H5LVWCCXX:5:2221:19442:38087
sOdqFxYPZI ... 0.2 0.2 60 ST-E00185:49:H5LVWCCXX:5:1121:14601:36452
sOdqFxYPZI 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:1113:26720:46859
sODqFxYPZI 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:1113:26568:46982
sODqFxYPZI 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2218:19158:69802
sOdqFxYPZI 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:2218:19219:69802
sOdqFxYPZI 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:1111:6410:24444
QUAL:8672.0
ekg commented
Updated further, so we don't have to do the --asume-ref trick to get the gap bases in the haps from the VCF.
1_3675803_C_CAATTATTTAAA
reference CACAAATTC-------
hap .-------
hap .AATTATT
geno .-------
geno .AATTATT
SodqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1211:15839:43273
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2123:29237:25728
SodqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2221:21645:44644
SodqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2115:6531:41462
sOdqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2209:10226:33692
sOdqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1211:17757:2575
SodqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2202:9749:37753
SodqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2216:7110:46578
sOdqfXYPZI A........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2109:3801:2346
SOdqFxYPZi .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1201:26466:51553
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2222:32231:48213
SODqFxyPZi .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2201:26131:48934
SoDqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2108:13413:29191
SoDqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1108:12215:30105
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1108:12226:30088
SodqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1205:3131:5651
SodqfXYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2224:2969:63842
sOdqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2204:8348:36417
sOdqfXYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1106:12205:20840
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1219:3913:29156
sOdqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:1211:11891:17236
SodqfXYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:5943:15232
SodqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2111:32475:3032
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1102:26963:17500
SoDqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1108:29521:38421
sOdqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:1218:3009:65776
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2106:5334:14283
SodqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2217:28851:9800
SodqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:2115:23553:44644
sOdqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2113:11738:53645
sODqFxYPZI .........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2113:11353:54032
SodqFxYPZI .........AATTATT 0.1 1.0 60 ST-E00185:49:H5LVWCCXX:5:1204:18366:71700
SodqfXYPZI ........------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2122:18752:23038
SodqFxYPZI ......... 0.1 0.1 60 ST-E00185:49:H5LVWCCXX:5:2110:10439:38315
sOdqFxYPZI ......... 0.1 0.1 60 ST-E00185:49:H5LVWCCXX:5:2108:32211:52327
sOdqFxYPZI .------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2122:5719:41814
sOdqfXYPZI .------- 1.0 0.1 60 ST-E00185:49:H5LVWCCXX:5:2221:19442:38087
sOdqFxYPZI ... 0.0 0.0 60 ST-E00185:49:H5LVWCCXX:5:1121:14601:36452
QUAL:8672.0