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Handle new splice effects in ensembl-vep version 105 #320

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merged 1 commit into from
Nov 7, 2022

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GFJHogue
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Per https://github.com/Ensembl/ensembl-vep/releases/tag/release%2F105.0 there are 3 new effect terms in VEP that need handling.

  • splice_donor_5th_base_variant (SO:0001787)
  • splice_donor_region_variant (SO:0002170)
  • splice_polypyrimidine_tract_variant (SO:0002169)

I set the priority to match splice_region_variant (see the severity order here: https://useast.ensembl.org/info/genome/variation/prediction/predicted_data.html).

@ckandoth ckandoth self-assigned this Nov 7, 2022
@ckandoth ckandoth merged commit dacbb68 into mskcc:main Nov 7, 2022
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ckandoth commented Nov 7, 2022

Sorry for the late response. I left mskcc, but apparently the repo is still my responsibility. :) The edits look appropriate. Thanks!

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