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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
74 stars 18 forks source link

Phased models bugged? #126

Open dnil opened 7 months ago

dnil commented 7 months ago 
[daniel.nilsson@hasta-login:~/tmp/F0056610-lrs]└2 [D_telo_DN] 1m36s 1 $ genmod annotate ~/tmp/F0056610-lrs/2023-34375-05.vcf --annotate_regions | genmod models - -f ~/tmp/F0056610-lrs/abnormalhyena.fam -t ped -p 10 -o ~/tmp/F0056610-lrs/2023-34375-05.models.vcf --phased
Process VariantAnnotator-2:
Traceback (most recent call last):
  File "/home/daniel.nilsson/.conda/envs/D_telo_DN/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/home/daniel.nilsson/sandbox/genmod/genmod/annotate_models/variant_annotator.py", line 127, in run
    if variant['annotation']:
       ~~~~~~~^^^^^^^^^^^^^^
KeyError: 'annotation'