| --- |
| pretty_name: scAncestry Reference Panel |
| license: other |
| viewer: false |
| tags: |
| - genomics |
| - ancestry |
| - single-cell |
| - human |
| - hg38 |
| - gnomad |
| - 1000-genomes |
| - hgdp |
| --- |
| |
| # scAncestry Reference Panel |
|
|
| Reference data for [`scancestry`](https://github.com/powellgenomicslab/scancestry), a tool for inferring genetic ancestry from single-cell genomics data. |
|
|
| Reference genome build: **GRCh38 / hg38**. |
|
|
| ## Contents |
|
|
| This dataset bundles imputation, phasing, and population-reference files used by the scAncestry pipeline: |
|
|
| - `gnomad.genomes.v3.1.2.hgdp_tgp.miss0.01.maf0.01.vcf.gz` (+ `.tbi`) — gnomAD v3.1.2 HGDP+1000G common variants, used for PCA reference |
| - `gnomad.genomes.v3.1.2.hgdp_tgp.miss0.01.maf0.01.geno.gz` — same variants in LASER/TRACE `.geno` format (decompressed client-side at download) |
| - `gnomad.genomes.v3.1.2.hgdp_tgp.miss0.01.maf0.01.pruned.RefPC.coord` — pre-computed reference PC coordinates for TRACE |
| - `gnomad.genomes.v3.1.2.hgdp_tgp.phased_rare_snps.ancestry.miss0.05_updated_ids_updated_freqs_af01.frq` — population allele frequencies for fastNGSadmix |
| - `gnomad.genomes.v3.1.2.hgdp_tgp.phased_rare_snps.ancestry.miss0.05_updated_ids.nInd` — per-population sample counts for fastNGSadmix |
| - `ref_ancestries_dt.csv` — sample-to-population mapping for plotting |
| - `ref_vcfs_glimpse/` — per-chromosome phased reference VCFs for GLIMPSE imputation |
| - `ref_vcfs_cellsnplite_chr/`, `ref_vcfs_cellsnplite_non_chr/` — TOPMed-derived candidate-SNP VCFs for cellsnp-lite (two builds: `chr1`-style and `1`-style notation) |
| - `glimpse_chunks/` — GLIMPSE imputation chunk definitions and per-chromosome genetic maps |
| - `chr_vcf_locations_*.csv`, `glimpse_chunks.csv` — manifest CSVs consumed by the pipeline (path placeholders are rewritten client-side at download) |
| - `chr_names_mapping_chr_nonchr.txt` — chromosome name mapping between UCSC and Ensembl/NCBI styles |
| - `checksums.md5` — MD5 hashes for all files; validated client-side at download |
|
|
| Total size: ~185 GiB on this repo, expanding to ~273 GiB on disk after the bundled `.geno.gz` is decompressed. |
|
|
| ## Usage |
|
|
| The intended way to use this dataset is via the scAncestry tool's downloader script, which also runs the post-download validation, decompression, and path-rewriting steps: |
|
|
| ```bash |
| SIF=/path/to/scancestry_0.3.0.sif |
| singularity exec "$SIF" /scancestry/scripts/download_ref.sh /path/to/ref_data |
| ``` |
|
|
| To download the raw files directly without post-processing: |
|
|
| ```bash |
| hf download powellgenomicslab/scancestry-reference-data \ |
| --repo-type dataset --local-dir /path/to/ref_data |
| ``` |
|
|
| If you take this path you'll need to do the post-processing yourself (or via `singularity exec "$SIF" /scancestry/scripts/configure_ref.sh /path/to/ref_data`). |
|
|
| ## Provenance & licensing |
|
|
| The data here is derived from several public human-genetics resources. **Each source has its own terms that propagate through this dataset**; by using this data you agree to comply with the upstream licenses. |
|
|
| - **[gnomAD v3.1.2](https://gnomad.broadinstitute.org/)** — Broad Institute. Public release; see [gnomAD terms](https://gnomad.broadinstitute.org/terms). |
| - **[1000 Genomes Project](https://www.internationalgenome.org/)** — International Genome Sample Resource. Public-use data; see [IGSR data reuse policy](https://www.internationalgenome.org/IGSR_disclaimer). |
| - **[HGDP (Human Genome Diversity Project)](https://www.hagsc.org/hgdp/)** — Stanford / CEPH. Public release through gnomAD. |
| - **[TOPMed](https://topmed.nhlbi.nih.gov/)** — used here for candidate-SNP coordinates only (no genotype data). See [TOPMed data use terms](https://topmed.nhlbi.nih.gov/data-access). |
| - **[GLIMPSE](https://odelaneau.github.io/GLIMPSE/) genetic maps** — bundled per-chromosome from the GLIMPSE project. |
|
|
| ## Citation |
|
|
| If you use this dataset, please cite the scAncestry tool and the underlying resources: |
|
|
| ```bibtex |
| @software{scancestry, |
| title = {scAncestry: genetic ancestry inference from single-cell genomics data}, |
| url = {https://github.com/powellgenomicslab/scancestry}, |
| year = {2026} |
| } |
| |
| @article{karczewski2020gnomad, |
| title = {The mutational constraint spectrum quantified from variation in 141,456 humans}, |
| author = {Karczewski, Konrad J. and others}, |
| journal = {Nature}, |
| volume = {581}, |
| pages = {434--443}, |
| year = {2020}, |
| doi = {10.1038/s41586-020-2308-7} |
| } |
| |
| @article{1000genomes2015global, |
| title = {A global reference for human genetic variation}, |
| author = {{1000 Genomes Project Consortium}}, |
| journal = {Nature}, |
| volume = {526}, |
| pages = {68--74}, |
| year = {2015}, |
| doi = {10.1038/nature15393} |
| } |
| |
| @article{bergstrom2020hgdp, |
| title = {Insights into human genetic variation and population history from 929 diverse genomes}, |
| author = {Bergstr{\"o}m, Anders and others}, |
| journal = {Science}, |
| volume = {367}, |
| pages = {eaay5012}, |
| year = {2020}, |
| doi = {10.1126/science.aay5012} |
| } |
| |
| @article{rubinacci2021glimpse, |
| title = {Efficient phasing and imputation of low-coverage sequencing data using large reference panels}, |
| author = {Rubinacci, Simone and others}, |
| journal = {Nature Genetics}, |
| volume = {53}, |
| pages = {120--126}, |
| year = {2021}, |
| doi = {10.1038/s41588-020-00756-0} |
| } |
| ``` |
|
|
| ## Versioning |
|
|
| This dataset is a snapshot bundled with scAncestry release 0.3.0. Future updates will be tagged on the repository. |
|
|
