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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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END position changed between delly 1.1.6 and 1.1.7 #357

Closed Stikus closed 6 months ago

Stikus commented 6 months ago

Hello, thanks for great tool.

Our test results have changed between delly versions 1.1.6 and 1.1.7:

< 19    2015016 DEL00000000 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2015363;PE=2;MAPQ=60;CT=3to5;CIPOS=-209,209;CIEND=-209,209 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-9.29073,0,-39.2907:93:PASS:5560:7646:1531:2:7:2:0:0
< 19    2050452 DEL00000001 G   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2050805;PE=2;MAPQ=60;CT=3to5;CIPOS=-179,179;CIEND=-179,179 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-6.28044,0,-96.2804:63:PASS:7094:14091:4353:2:17:2:0:0
< 19    2060992 DEL00000002 A   <DEL>   180 PASS    IMPRECISE;SVTYPE=DEL;END=2061315;PE=3;MAPQ=60;CT=3to5;CIPOS=-152,152;CIEND=-152,152 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-9.57117,0,-141.571:96:PASS:6977:10917:4278:2:25:3:0:0
< 19    2101808 DEL00000003 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2102177;PE=2;MAPQ=60;CT=3to5;CIPOS=-257,257;CIEND=-257,257 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-1.16293,0,-193.163:12:LowQual:8323:14865:6588:2:34:2:0:0
< 19    2116045 DEL00000004 G   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2116378;PE=2;MAPQ=60;CT=3to5;CIPOS=-205,205;CIEND=-205,205 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-10.7753,0,-118.775:108:PASS:6703:12259:6162:2:21:3:0:0
< 19    2128104 DEL00000005 C   <DEL>   89  LowQual IMPRECISE;SVTYPE=DEL;END=2128466;PE=2;MAPQ=60;CT=3to5;CIPOS=-227,227;CIEND=-227,227 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-2.57838,0,-107.679:26:PASS:7162:9862:2266:2:19:2:0:0
< 19    2128599 DEL00000006 A   <DEL>   540 PASS    IMPRECISE;SVTYPE=DEL;END=2129045;PE=9;MAPQ=60;CT=3to5;CIPOS=-67,67;CIEND=-67,67 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-56.1281,-3.23944,0:32:PASS:3084:809:5685:0:0:11:0:0
< 19    2136120 DEL00000007 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2136448;PE=2;MAPQ=60;CT=3to5;CIPOS=-237,237;CIEND=-237,237 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-10.7753,0,-118.775:108:PASS:5607:12689:5984:2:21:3:0:0
< 19    2168904 DEL00000008 T   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2169248;PE=2;MAPQ=60;CT=3to5;CIPOS=-219,219;CIEND=-219,219 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-2.96911,0,-158.969:30:PASS:6970:14186:6486:2:28:2:0:0
< 19    2173248 DEL00000009 T   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2173640;PE=2;MAPQ=60;CT=3to5;CIPOS=-176,176;CIEND=-176,176 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-3.27014,0,-153.27:33:PASS:6405:15184:8252:2:27:2:0:0
---
> 19    2015016 DEL00000000 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2015362;PE=2;MAPQ=60;CT=3to5;CIPOS=-209,209;CIEND=-209,209 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-9.29073,0,-39.2907:93:PASS:5560:7646:1531:2:7:2:0:0
> 19    2050452 DEL00000001 G   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2050804;PE=2;MAPQ=60;CT=3to5;CIPOS=-179,179;CIEND=-179,179 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-6.28044,0,-96.2804:63:PASS:7094:14091:4353:2:17:2:0:0
> 19    2060992 DEL00000002 A   <DEL>   180 PASS    IMPRECISE;SVTYPE=DEL;END=2061314;PE=3;MAPQ=60;CT=3to5;CIPOS=-152,152;CIEND=-152,152 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-9.57117,0,-141.571:96:PASS:6977:10917:4278:2:25:3:0:0
> 19    2101808 DEL00000003 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2102176;PE=2;MAPQ=60;CT=3to5;CIPOS=-257,257;CIEND=-257,257 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-1.16293,0,-193.163:12:LowQual:8323:14865:6588:2:34:2:0:0
> 19    2116045 DEL00000004 G   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2116377;PE=2;MAPQ=60;CT=3to5;CIPOS=-205,205;CIEND=-205,205 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-10.7753,0,-118.775:108:PASS:6703:12259:6162:2:21:3:0:0
> 19    2128104 DEL00000005 C   <DEL>   89  LowQual IMPRECISE;SVTYPE=DEL;END=2128465;PE=2;MAPQ=60;CT=3to5;CIPOS=-227,227;CIEND=-227,227 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-2.57838,0,-107.679:26:PASS:7162:9862:2266:2:19:2:0:0
> 19    2128599 DEL00000006 A   <DEL>   540 PASS    IMPRECISE;SVTYPE=DEL;END=2129044;PE=9;MAPQ=60;CT=3to5;CIPOS=-67,67;CIEND=-67,67 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 1/1:-56.1281,-3.23944,0:32:PASS:3084:809:5685:0:0:11:0:0
> 19    2136120 DEL00000007 C   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2136447;PE=2;MAPQ=60;CT=3to5;CIPOS=-237,237;CIEND=-237,237 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-10.7753,0,-118.775:108:PASS:5607:12689:5984:2:21:3:0:0
> 19    2168904 DEL00000008 T   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2169247;PE=2;MAPQ=60;CT=3to5;CIPOS=-219,219;CIEND=-219,219 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-2.96911,0,-158.969:30:PASS:6970:14186:6486:2:28:2:0:0
> 19    2173248 DEL00000009 T   <DEL>   120 LowQual IMPRECISE;SVTYPE=DEL;END=2173639;PE=2;MAPQ=60;CT=3to5;CIPOS=-176,176;CIEND=-176,176 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-3.27014,0,-153.27:33:PASS:6405:15184:8252:2:27:2:0:0

The only difference is END change: 2015363 -> 2015362 for example. Is this intended? Cannot find any info (and changelog :( )

tobiasrausch commented 6 months ago

Yes, that's intended. So far delly used the last aligned base which makes more sense for complex rearrangements, translocations, etc. but for deletions this makes delly incompatible with bcftools norm --check-ref ... or bcftools consensus .... Since for the new long-read mode this is a common downstream task I had to change this coordinate.

Stikus commented 6 months ago

Thank you for fast answer. I'll close issue.