bigbio/hvantk

Hail variant annotation toolkit

Stars: 1
Forks: 0
Open beginner issues: 0
Indexed issues: 20
Avg merge: 1d 3h
Merged PRs (30d): 40

Dominant language: Python
License: MIT
Last GitHub push: Sep 7, 2026
Latest indexed: Sep 14, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Open All

20 open issues indexed

PTM-EDA: PhosphoSitePlus LTP-tier stratification to test functional-site vs detection-bias signal Open

enhancement

bigbio/hvantk#95 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Validate plugin-author UX: walk one new plugin through agent-driven authoring Open

bigbio/hvantk#112 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Declare plugin data-acquisition policy explicitly in plugin.yaml Open

bigbio/hvantk#118 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Follow-up: deferred review findings from release #184 (catalog metadata + minor polish) Open

enhancement

bigbio/hvantk#185 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
PTM dataset build path: uniprot-ptm key bug, cptac reprocess wiring, deps & resilience Open

bigbio/hvantk#198 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
HGC QC: cap the module at computation; retire the QC plotting layer Open

clean-up

bigbio/hvantk#205 · 0 comments · 1 reaction · 2 assignees · Indexed Sep 14, 2026
burden: make _driver_af tie-break deterministic (needs CHD gate re-run) Open

bigbio/hvantk#230 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
insider: move the variants dataset into its own subfolder (complete the multi-dataset layout) Open

bigbio/hvantk#232 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
rerank: port the multiplicity control, blocked CV and seed handling into the library Open

bigbio/hvantk#247 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
drift: uniprot_ptm cannot detect a UniProt release; hgnc/gencc have no corroborating signal Open

bigbio/hvantk#271 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
cli: _LAZY_COMMANDS duplicates the tool.yaml registry, and 14/18 descriptions already disagree Open

enhancement

bigbio/hvantk#304 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
cli: LazyGroup loses lazy shell completion and "Did you mean" suggestions Open

bug

bigbio/hvantk#305 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
cli: hgc/enrichex/qtlcascade subgroups still import Hail to render --help Open

enhancement

bigbio/hvantk#306 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
ptm: export_ptm_strata still makes 3 full passes, and its new comment overstates the cause Open

enhancement psroc

bigbio/hvantk#307 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
enrichex/qtlcascade: duplication left behind by the #303 de-duplication pass Open

enhancement

bigbio/hvantk#308 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
tooling: decide on ruff format, and on enabling B/S so the existing noqas stop being inert Open

question

bigbio/hvantk#309 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Drift probes failing Open

drift:probe-failed

bigbio/hvantk#312 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
statsmodels is imported at module scope but declared in no dependency set Open

bug

bigbio/hvantk#318 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
dbNSFP: every documented download link is dead (S3 bucket no longer exists) Open

bigbio/hvantk#321 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
drift: HEAD-only probes tier every upstream release as a schema change, saturating drift:schema Open

enhancement

bigbio/hvantk#333 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026

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