dvitale199/GenoTools

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GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.

Stars: 37
Forks: 8
Open beginner issues: 0
Indexed issues: 31
Avg merge: 2h 23m
Merged PRs (30d): 21

Dominant language: Python
License: Apache-2.0
Last GitHub push: Sep 15, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

31 open issues indexed

No test covers the empty-CAS guard in _predict_admixed Open

correctness

Difficulty 3/5 1-2 days Newbie friendliness 72/100

dvitale199/GenoTools#294 · Opened Sep 15, 2026
"CAS" is hardcoded in the admixture step, but the label vocabulary is user-supplied Open

ancestry-quality correctness

Difficulty 5/5 Over a week Newbie friendliness 45/100

dvitale199/GenoTools#293 · Opened Sep 15, 2026
Ancestry predict path holds three full-size copies; nothing bounds the peak Open

perf refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 48/100

dvitale199/GenoTools#292 · Opened Sep 15, 2026
Retraining moves ~1.3% of labels: a plateaued grid search, not a race Open

ancestry-quality refactor-backlog

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

dvitale199/GenoTools#291 · Opened Sep 15, 2026
Persist cv_results_ as a record of model selection Open

refactor-backlog reporting

Difficulty 4/5 3-5 days Newbie friendliness 56/100

dvitale199/GenoTools#290 · Opened Sep 15, 2026
Cache the UMAP fits — the grid search recomputes each embedding six times Open

perf refactor-backlog

Difficulty 4/5 3-5 days Newbie friendliness 55/100

dvitale199/GenoTools#289 · Opened Sep 15, 2026
Supervised UMAP is asymmetric between fit and transform Open

ancestry-quality refactor-backlog

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

dvitale199/GenoTools#288 · Opened Sep 15, 2026
Does UMAP + gblinear earn its cost over a model-free baseline? Open

ancestry-quality refactor-backlog

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

dvitale199/GenoTools#287 · Opened Sep 15, 2026
TrainingConfig.n_jobs derives from machine RAM and CPU count, so run cost is not reproducible Open

perf refactor-backlog

Difficulty 3/5 1-2 days Newbie friendliness 65/100

dvitale199/GenoTools#286 · Opened Sep 15, 2026
Fit-validation thresholds are reasoned, not calibrated Open

ancestry-quality refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

dvitale199/GenoTools#285 · Opened Sep 15, 2026
Revisit updater=coord_descent only if XGBoost's linear updaters change Open

ancestry-quality refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 15/100

dvitale199/GenoTools#284 · Opened Sep 15, 2026
Audit released ancestry label sets for the collapse signature Open

ancestry-quality refactor-backlog

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

dvitale199/GenoTools#283 · Opened Sep 15, 2026
ancestry_diagnostics has no golden — regression goldens cover no ancestry run Open

refactor-backlog reporting

Difficulty 3/5 1-2 days Newbie friendliness 68/100

dvitale199/GenoTools#282 · Opened Sep 15, 2026
The ancestry self-test measures a floor, not accuracy Open

ancestry-quality refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

dvitale199/GenoTools#281 · Opened Sep 15, 2026
Ancestry diagnostic thresholds are reasoned, not calibrated Open

ancestry-quality refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

dvitale199/GenoTools#280 · Opened Sep 15, 2026
Ancestry training mode has no overlap report, and a width mismatch crashes it Open

correctness refactor-backlog reporting

Difficulty 3/5 1-2 days Newbie friendliness 74/100

dvitale199/GenoTools#279 · Opened Sep 15, 2026
JSON report records temp paths that no longer exist Open

refactor-backlog reporting

Difficulty 3/5 1-2 days Newbie friendliness 68/100

dvitale199/GenoTools#278 · Opened Sep 15, 2026
JSON report parameters section does not cover the non-QC settings Open

refactor-backlog reporting

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

dvitale199/GenoTools#277 · Opened Sep 15, 2026
No separate sample floor for heterozygosity sd mode Open

correctness refactor-backlog

Difficulty 4/5 3-5 days Newbie friendliness 38/100

dvitale199/GenoTools#276 · Opened Sep 15, 2026
--het-ancestry / --subset-ancestry labels are not validated until after prediction Open

correctness refactor-backlog

Difficulty 3/5 1-2 days Newbie friendliness 68/100

dvitale199/GenoTools#275 · Opened Sep 15, 2026
Skips are decided before the chain runs, so a precondition broken mid-chain is missed Open

correctness refactor-backlog

Difficulty 4/5 3-5 days Newbie friendliness 55/100

dvitale199/GenoTools#274 · Opened Sep 15, 2026
Tier 3 — automatic ancestry PCA cache, keyed on (ref_panel, common_snps) Open

perf refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

dvitale199/GenoTools#273 · Opened Sep 15, 2026
Tier 2 — parallelize per-ancestry QC groups Open

perf refactor-backlog

Difficulty 4/5 3-5 days Newbie friendliness 64/100

dvitale199/GenoTools#272 · Opened Sep 15, 2026
Decide the dependency-bound policy: float with CI as canary, or add upper bounds Open

infra refactor-backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

dvitale199/GenoTools#213 · 1 comment · Opened Jun 2, 2025
min sample error catching for --ld Open

correctness

Difficulty 3/5 1-2 days Newbie friendliness 65/100

dvitale199/GenoTools#178 · 2 comments · Opened Apr 24, 2024
Adjust gwas module to allow for any phenotype (not just PHENO1) Open

correctness

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

dvitale199/GenoTools#172 · 1 comment · Opened Mar 28, 2024
combine covars with PCs if --covars and --pca called Open

correctness enhancement

dvitale199/GenoTools#153 · 1 comment · 3 assignees · Opened Jan 5, 2024
ref_labels added as PHENO1 in ref panel Open

ancestry-quality enhancement

dvitale199/GenoTools#115 · 1 assignee · Opened Nov 15, 2023
Scree plot for ancestry PCA (eigenvalues already ship) Open

good first issue reporting

Difficulty 3/5 1-2 days Newbie friendliness 55/100

dvitale199/GenoTools#29 · 1 comment · Opened Aug 24, 2022
Liftover Open

enhancement

dvitale199/GenoTools#15 · 1 assignee · Opened Oct 29, 2021
Manhattan Plot Open

enhancement reporting

dvitale199/GenoTools#7 · 1 comment · 2 assignees · Opened Sep 22, 2021

dvitale199/GenoTools

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