README.md

---
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.