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Add support for VCFv4.2 breakend notation #79

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nvnieuwk opened this issue Mar 2, 2023 · 0 comments
Open

Add support for VCFv4.2 breakend notation #79

nvnieuwk opened this issue Mar 2, 2023 · 0 comments

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@nvnieuwk
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nvnieuwk commented Mar 2, 2023

Hi, thanks for this wonderful tool!

I'm wondering whether or not it is planned to add support for VCFv4.2 breakend notation as specified here? Currently the tool exits with the following error when trying to genotype a VCF using this notation:

    File "/usr/local/bin/multigrmpy.py", line 353, in <module>
      main()
    File "/usr/local/bin/multigrmpy.py", line 349, in main
      run(args)
    File "/usr/local/bin/multigrmpy.py", line 261, in run
      graph_files = load_graph_description(args)
    File "/usr/local/bin/multigrmpy.py", line 52, in load_graph_description
      header, records, event_list = convert_vcf_to_json(args, alt_paths=True)
    File "/usr/local/lib/python3/grm/vcf2paragraph/__init__.py", line 156, in convert_vcf_to_json
      variants = pool.map(run_vcf2paragraph, zip(to_process, itertools.repeat(params)))
    File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 268, in map
      return self._map_async(func, iterable, mapstar, chunksize).get()
    File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 657, in get
      raise self._value
  Exception: Illegal character in ALT allele: ]chr16:75595853]A
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