Coordinate <= 0 detected

[YiBenqiu]

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?

[HuTaoJiaZiAckerman]

I have the same question. Is there any way to solve it?