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Implement "seqvars prefilter" command #209

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holtgrewe opened this issue Oct 6, 2023 · 0 comments · Fixed by #213
Closed

Implement "seqvars prefilter" command #209

holtgrewe opened this issue Oct 6, 2023 · 0 comments · Fixed by #213
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enhancement New feature or request
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@holtgrewe
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Is your feature request related to a problem? Please describe.
Between seqvars ingest and seqvars query, it would be useful to have a command that downfilters the variants.

Describe the solution you'd like
Implement seqvars prefilter that takes seqvars ingest output and only keeps variants with

  • population frequency
  • exon distance

are below a threshold given on the command line. This allows to generate a number of prefiltered files after seqvars ingest which greatly reduce the I/O amount for queries that only consider <1% variants and <200bp exon distance anyway.

Describe alternatives you've considered
N/A

Additional context
N/A

@holtgrewe holtgrewe added the enhancement New feature or request label Oct 6, 2023
@holtgrewe holtgrewe linked a pull request Oct 9, 2023 that will close this issue
@holtgrewe holtgrewe added this to the v0.11.0 milestone Oct 19, 2023
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Labels
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