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llecompte / SVJedi

SV genotyping with long reads
GNU Affero General Public License v3.0
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Error when generating allele sequences from a VCF obtained with MANTA #13

Closed clemaitre closed 2 years ago

clemaitre commented 2 years ago

A bug reported by a user, with an input VCF file output by the SVcaller MANTA (after post-processing inversions with their script convertInversion.py).

For INV variants the END field in info is in first position, which causes the following error:

File "modules/generateRef.py", line 125, in create_ref
    end = int(info.split(';END=')[1].split(';')[0])
IndexError: list index out of range