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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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"Unknown Impacts": splice_donor_5th_base, splice_donor_region, splice_polypyrimidine_tract #157

Closed wwgordon closed 9 months ago

wwgordon commented 9 months ago

Hi Brent,

The current default VEP annotation appears to include 3 Consequences not contained in default-order.txt:

splice_donor_5th_base splice_donor_region splice_polypyrimidine_tract

They all have IMPACT == LOW:

http://useast.ensembl.org/info/genome/variation/prediction/predicted_data.html#consequences

I am using VEP version 110:

Versions:
  ensembl              : 110.584a8f3
  ensembl-funcgen      : 110.24e6da6
  ensembl-io           : 110.b1a0d57
  ensembl-variation    : 110.d34d25e
  ensembl-vep          : 110.1

I've added them to my custom *order.txt but thought you'd like to know.

On a minor note, the warning states:

warning: unknown impact "splice_polypyrimidine_tract" from csq "TAAA|splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|..." please report the variant at https://github.com/brentp/slivar/issues

...however I believe this is actually an unknown Consequence; the IMPACT is known ("LOW").

Cheers, William

brentp commented 9 months ago

thanks for reporting, I have added these to the repo. The message means it's unknown to slivar, which does not exactly rely on the impact given by the tool.