cancervariants / cancervariants/variation-normalization

gnomad_vcf_to_protein warnings for intron variants

Open
#284 3 comments 0 reactions 0 assignees View on GitHub
enhancement priority:low
Dominant language
Python
Stars
15
Forks
2
PR merge metrics
No merged PRs in 30d

Description

`variation/gnomad_vcf_to_protein?q=7-55142262-G-A` returns `Unable to get transcripts given NC_000007.14 and 55142262` in its warnings. This is because it maps to a location on an intron rather than an exon. It'd be more useful to have the warnings contain a message saying that it's unable to translate to protein variation since it's an intron variant

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by calling the variation/gnomad_vcf_to_protein endpoint with q=7-55142262-G-A and trace where its warnings are assembled. Update the warning for an intron mapping to state that the variant cannot be translated to a protein variation, then verify that this input produces the clearer message.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
api, bioinformatics
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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