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Cannot handle new Dragen CNV VCF files #557

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holtgrewe opened this issue Oct 7, 2024 · 0 comments
Open

Cannot handle new Dragen CNV VCF files #557

holtgrewe opened this issue Oct 7, 2024 · 0 comments
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bug Something isn't working

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@holtgrewe
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holtgrewe commented Oct 7, 2024

Describe the bug
The new DRAGEN CNV VCF files provide reference-only records, see below. These don't have an INFO/SVTYPE entry. Mehari strucvars annotation fails with "SVTYPE not found".

1       123  DRAGEN:REF:1:123-345     N       .       .       SampleFT        END=345;REFLEN=xxx

To Reproduce
Steps to reproduce the behavior:

  1. Annotate such a file.
  2. See crash.

Expected behavior
These reference-only lines should be skipped.

In case of issues because of non-complying with . in <*> and noodles, handle them appropriately.

The deviating behaviour should be documented, at least in the source code API documentation, ideally in README.

Additional context
N/A

@holtgrewe holtgrewe added the bug Something isn't working label Oct 7, 2024
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