Human Diversity Reference (DivRef)
Description
Human diversity reference (DivRef) bundle
This resource bundle contains a custom human diversity reference (DivRef) composed of short base sequences around common variation in the human population, with a tool for remapping coordinates from this custom reference back to GRCh38.
DivRef is constructed by computing empirical phased haplotypes within 25 BPs over 0.5% allele frequency from the Human Genome Diversity Panel (HGDP) using the phased Hail dataset provided by the gnomAD team at the Broad Institute, merged with single variants over 0.5% AF from the gnomAD v4.1.0 summary release. The base context including and surrounding these variants and haplotypes is generated from the GRCh38 reference sequence, and each variant and haplotype is exported to a FASTA file. These FASTA files are intended to be used with tools for guide design and off-target nomination that already accept reference sequences as FASTA files.
From the team at E9 Genomics.
Changelog:
- v1.1 (2025/02/12)
- Updated haplotype filtering algorithm to improve discovery of haplotypes <= 1% AF, which added ~200k haplotypes.
- Fixed bug in `remap_divref.py` script
Files
README.md
Files
(8.3 GB)
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Additional details
Dates
- Created
-
2025-01-24
- Updated
-
2025-02-12
Software
- Repository URL
- https://github.com/e9genomics/human-diversity-reference