Dear developers.
When I use svimmer to merge the vcf created by manta. I found some warnings in the log file.
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
This is probably due to the position becoming from 0 after converting the INV variant type with the convertInversion.py script supported by manta.
Here is an example created by manta (diploidSV.vcf.gz)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1
1 1 MantaBND:82572:0:1:0:0:0:0 G [1:5440[G 279 PASS SVTYPE=BND;MATEID=MantaBND:82572:0:1:0:0:0:1;CIPOS=0,2;HOMLEN=2;HOMSEQ=CT;BND_DEPTH=12;MATE_BND_DEPTH=14
1 5438 MantaBND:82572:0:1:0:0:0:1 G [1:3[G 279 PASS SVTYPE=BND;MATEID=MantaBND:82572:0:1:0:0:0:0;CIPOS=0,2;HOMLEN=2;HOMSEQ=CA;BND_DEPTH=14;MATE_BND_DEPTH=12
After converting, the position changed to 0:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1
1 0 MantaINV:82572:0:1:0:0:0 <INV> 279 PASS END=5439;SVTYPE=INV;SVLEN=5439;CIPOS=0,2;CIEND=-2,0;HOMLEN=2;HOMSEQ=GC;INV5 GT:FT:GQ:PL:PR:SR
This result may caused "[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?"
Does this warning have a bad effect on the merged.vcf.gz results?
Dear developers. When I use svimmer to merge the vcf created by manta. I found some warnings in the log file.
This is probably due to the position becoming from 0 after converting the INV variant type with the convertInversion.py script supported by manta.
Here is an example created by manta (diploidSV.vcf.gz)
After converting, the position changed to 0:
This result may caused "[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?" Does this warning have a bad effect on the merged.vcf.gz results?