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VCF 4.2 compatibility #183

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b-schubert opened this issue Nov 14, 2016 · 3 comments
Open

VCF 4.2 compatibility #183

b-schubert opened this issue Nov 14, 2016 · 3 comments
Milestone
Release 2.0

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@b-schubert
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It would be great to generalize the variant reader to VCF 4.2:

Possible problems:

  • Different annotation tools use slightly different annotations in the comment column
  • Check that for at least SnepEff, and VEP
  • Annova still does not support direct VCF 4.2 input
@b-schubert b-schubert added this to the Release 2.0 milestone Nov 14, 2016
@b-schubert
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@mwalzer Do you know if pyVCF can use the annotation coming from SnepEff and VEP?

@b-schubert
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see PR #184

@mwalzer
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mwalzer commented Feb 2, 2017 •
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I did not test VEP specifically, but pyVCF can do 4.1 for now, also from files of SnepEff.

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@mwalzer @b-schubert