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get_mnv.py fails to import vcf #1

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kvn95ss opened this issue Feb 15, 2021 · 0 comments
Open

get_mnv.py fails to import vcf #1

kvn95ss opened this issue Feb 15, 2021 · 0 comments

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@kvn95ss
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kvn95ss commented Feb 15, 2021

Hello,

I'm trying to run this pipeline on a dataset (currently restricted to 10 singleton exomes) but hail fails to import the vcf file and throws the following error -

TypeError: 'split_multi_hts': Found invalid types for the following fields:
  'PGT' found: str      expected: call

I modified the import code from

vcf = hl.import_vcf(sys.argv[1], call_fields=["GT"]) 

to

vcf = hl.import_vcf(sys.argv[1]) 

And now my vcf loads into hail and the mt files are generated. However, I would just like to know if the modification would break something down the line, or whether the modification was an okay thing to do.

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