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
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: