cancervariants/variation-normalization

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Services and guidelines for normalizing variants

Stars: 15
Forks: 2
Open beginner issues: 0
Indexed issues: 70

Dominant language: Python
License: MIT
Last GitHub push: Jul 24, 2026
Latest indexed: Sep 14, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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70 open issues indexed

Add support for cdna duplications Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 62/100

cancervariants/variation-normalization#674 · Opened Jul 24, 2026
VRS ID mismatches for same concept Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

cancervariants/variation-normalization#672 · 1 comment · Opened Jul 22, 2026
Docker image crashes Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#671 · Opened Jul 22, 2026
Various variants unable to be normalized Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

cancervariants/variation-normalization#667 · 1 comment · Opened Apr 30, 2026
Version is not showing Open

bug priority:high

Difficulty 3/5 1-2 days Newbie friendliness 58/100

cancervariants/variation-normalization#662 · 6 comments · Opened Apr 6, 2026
Unable to normalize HIST1H3B K28M Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

cancervariants/variation-normalization#661 · 1 comment · Opened Mar 25, 2026
Add `/service-info` Open

enhancement priority:medium

Difficulty 3/5 1-2 days Newbie friendliness 38/100

cancervariants/variation-normalization#660 · Opened Mar 17, 2026
Frameshift variants should not return valid VRS objects in gnomad_vcf_to_protein Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cancervariants/variation-normalization#652 · 1 comment · Opened Feb 27, 2026
Add support for transcript variant normalization Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

cancervariants/variation-normalization#632 · 1 comment · Opened Oct 27, 2025
Normalization works on some NCBI 36 Variants Open

bug priority:low

cancervariants/variation-normalization#628 · 1 comment · 1 assignee · Opened Aug 7, 2025
Postgres query errors for compose.yaml when under parallel load due to low `shm_size` default Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cancervariants/variation-normalization#627 · 1 comment · Opened Aug 6, 2025
missing hgnc id for several variants Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#624 · 2 comments · Opened Jul 28, 2025
Better error handling: FastAPI Open

enhancement priority:high

cancervariants/variation-normalization#617 · 1 assignee · Opened Jul 16, 2025
Add `moleculeType` to `SequenceReference` Open

enhancement priority:low

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cancervariants/variation-normalization#594 · 1 comment · Opened Jan 20, 2025
return gene context info for genomic queries Open

enhancement priority:low

cancervariants/variation-normalization#551 · 11 comments · 1 assignee · Opened Mar 27, 2024
Reduce the number of tests Open

priority:low test

Difficulty 5/5 Over a week Newbie friendliness 20/100

cancervariants/variation-normalization#527 · 2 comments · Opened Jan 10, 2024
Use biocommons.hgvs for parsing HGVS expressions Open

build priority:medium technical debt

Difficulty 4/5 3-5 days Newbie friendliness 25/100

cancervariants/variation-normalization#526 · 2 comments · Opened Dec 11, 2023
Consider lazy loading for class attributes Open

priority:low technical debt

Difficulty 4/5 3-5 days Newbie friendliness 30/100

cancervariants/variation-normalization#522 · 2 comments · Opened Nov 7, 2023
Add basic API endpoint tests Open

priority:medium test

Difficulty 3/5 1-2 days Newbie friendliness 25/100

cancervariants/variation-normalization#519 · 2 comments · Opened Oct 26, 2023
If genomic query fails getting liftover/mane, try using original input to return a response Open

enhancement priority:medium

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#506 · 3 comments · Opened Sep 1, 2023
Stabilize construction of required resources Open

priority:low technical debt

Difficulty 5/5 Over a week Newbie friendliness 25/100

cancervariants/variation-normalization#499 · 2 comments · Opened Aug 22, 2023
Add support for SPDI nomenclature in /to_vrs and /normalize Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

cancervariants/variation-normalization#497 · Opened Aug 22, 2023
Considering adding vulture pre-commit hook Open

build priority:low

Difficulty 3/5 1-2 days Newbie friendliness 38/100

cancervariants/variation-normalization#493 · 3 comments · 1 reaction · Opened Aug 21, 2023
Parameterize `vrs_ref_allele_seq` Open

enhancement

cancervariants/variation-normalization#481 · 1 comment · 1 assignee · Opened Aug 8, 2023
Improve free text query performance Open

performance priority:high

cancervariants/variation-normalization#477 · 4 comments · 1 assignee · Opened Jul 31, 2023
Add more tests for HGVS Ensembl expressions Open

priority:low test

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cancervariants/variation-normalization#471 · 2 comments · Opened Jul 20, 2023
Better error and warning handling Open

priority:medium technical debt

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#467 · 3 comments · Opened Jul 18, 2023
Add FAQ Docs Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

cancervariants/variation-normalization#466 · Opened Jul 14, 2023
Parsed to CNV endpoints do not cover all ambiguous ranges Open

bug priority:low

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#465 · 1 comment · Opened Jul 13, 2023
Add support for NG expressions Open

enhancement priority:low

Difficulty 5/5 Over a week Newbie friendliness 30/100

cancervariants/variation-normalization#464 · 1 comment · Opened Jul 13, 2023
hgvs_to_copy_number_count should support 0 baseline_copies Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

cancervariants/variation-normalization#457 · 1 comment · 1 reaction · Opened Jun 28, 2023
parsed to copy number endpoints should allow curie or gene as subject Open

enhancement priority:low

Difficulty 3/5 1-2 days Newbie friendliness 30/100

cancervariants/variation-normalization#451 · 1 comment · Opened Jun 21, 2023
to_vrs returns valid results when hgvs position is greater than ref sequence length Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cancervariants/variation-normalization#449 · 2 comments · Opened Jun 19, 2023
Update FastAPI descriptions Open

documentation

cancervariants/variation-normalization#448 · 1 assignee · Opened Jun 17, 2023
/parsed_to_cn_var should accept number, indefinite range, or definite range Open

bug priority:low

cancervariants/variation-normalization#443 · 3 comments · 1 assignee · Opened Jun 2, 2023
server error on /to_vrs and /normalize for "NC_000010.11-87925523-C-G" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cancervariants/variation-normalization#438 · 1 comment · Opened May 30, 2023
Add more tests for incorrect input Open

priority:low test

Difficulty 3/5 1-2 days Newbie friendliness 35/100

cancervariants/variation-normalization#436 · 1 comment · Opened May 25, 2023
Add support for HGVS insertions of form {pos}_{pos}ins{pos}_{pos} Open

bug enhancement priority:low

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cancervariants/variation-normalization#434 · 1 comment · Opened May 19, 2023
Add support for more ambiguous deletions + duplications Open

enhancement priority:high

cancervariants/variation-normalization#420 · 3 comments · 1 assignee · Opened May 8, 2023
parsed_to_cn_var should support total_copies ranges Open

enhancement priority:low

Difficulty 3/5 1-2 days Newbie friendliness 45/100

cancervariants/variation-normalization#418 · 2 comments · Opened May 8, 2023
Update to_vrs API description Open

documentation priority:low

Difficulty 1/5 Under an hour Newbie friendliness 35/100

cancervariants/variation-normalization#416 · 2 comments · Opened May 5, 2023
Add readthedocs Open

documentation priority:medium

cancervariants/variation-normalization#407 · 4 comments · 1 assignee · Opened Apr 26, 2023
Use FastAPIRouter Open

priority:low technical debt

cancervariants/variation-normalization#398 · 1 comment · 1 assignee · Opened Apr 7, 2023
Add lucid diagram to docs Open

documentation priority:low

Difficulty 3/5 1-2 days Newbie friendliness 25/100

cancervariants/variation-normalization#364 · 2 comments · Opened Jan 27, 2023
Add support for HGVS c. queries on intronic site and translate to protein representation Open

enhancement priority:high

cancervariants/variation-normalization#357 · 3 comments · 1 assignee · Opened Jan 11, 2023
Add support for (#_?)_(?_#) ambiguous ranges Open

enhancement priority:high requirement

cancervariants/variation-normalization#342 · 4 comments · 1 assignee · Opened Nov 9, 2022
gnomad_vcf_to_protein warnings for intron variants Open

enhancement priority:low

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

cancervariants/variation-normalization#284 · 3 comments · Opened Apr 26, 2022
Follow Conventional Commit Spec Open

chore ci/cd priority:low

cancervariants/variation-normalization#283 · 1 comment · 1 assignee · Opened Apr 20, 2022
Insertions that are dups should be classified as duplications Open

bug priority:low

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#281 · 3 comments · Opened Apr 19, 2022
Fix bugs with Ensembl support Open

bug priority:low

Difficulty 4/5 3-5 days Newbie friendliness 35/100

cancervariants/variation-normalization#248 · 2 comments · Opened Feb 24, 2022

cancervariants/variation-normalization

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