Question about inversion and problem with convertInversion.py script

[ptranvan]

Hi,

Based on https://github.com/Illumina/manta/tree/master/docs/userGuide#inversions:

1) I don't understand why do you report four breakends for an inversion ?

2) I tried to execute the script convertInversion.pyand got an issue:

Traceback (most recent call last):
  File "/Users/admin/Documents/software/manta-1.6.0.centos6_x86_64/libexec/convertInversion.py", line 291, in <module>
    convertInversions(samtools, refFasta, vcfFile, invMateDict)
  File "/Users/admin/Documents/software/manta-1.6.0.centos6_x86_64/libexec/convertInversion.py", line 175, in convertInversions
    vcfRec.chr, vcfRec.pos, vcfRec.pos)
  File "/Users/admin/Documents/software/manta-1.6.0.centos6_x86_64/libexec/convertInversion.py", line 121, in getReference
    samtoolsOut = check_output([samtools, "faidx", refFasta, region])
  File "/Users/admin/miniconda2/lib/python2.7/subprocess.py", line 212, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/Users/admin/miniconda2/lib/python2.7/subprocess.py", line 390, in __init__
    errread, errwrite)
  File "/Users/admin/miniconda2/lib/python2.7/subprocess.py", line 1025, in _execute_child
    raise child_exception

any solution please ?

3) I am looking for inversions, diploidSV.vcf.gz is the right output to look at right ?

4) Inversion is SVTYPE=BND right ? This is my kind of result and I don't understand because I don't have the same information your guilde (ex: no EVENT)

Scaffold03 1185154 MantaBND:0:205:206:0:0:0:1 T [Scaffold03:1330424[ACAATACAATATAT 999 MaxDepth SVTYPE=BND;MATEID=MantaBND:0:205:206:0:0:0:0;SVINSLEN=13;SVINSSEQ=ACAATACAATATA;BND_DEPTH=28;MATE_BND_DEPTH=35 GT:FT:GQ:PL:PR:SR 0/1:PASS:193:999,0,190:14,23:8,24

Thanks a lot for your help.