[genome-announce] Phased variants track for human (hg38 and hg19)

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Jairo Navarro Gonzalez

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Feb 9, 2026, 7:18:25 PMFeb 9
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Hello everyone,

We are pleased to announce the release of the Phased Variants container track for hg38/GRCh38 and hg19/GRCh19. This new track brings together phased individual-level genotype data from four projects: Human Diversity Genome Project, Simons Genome Diversity Project, gnomad's HGDP+1000 Genomes callset, and the Mexico Biobank.

The Phased Variants track includes the following subtracks:

  • Mexico Biobank (MXB) 6k Array – Phased alleles from array genotyping of 6,011 individuals sampled across all 32 states of Mexico during the 2000 National Health Survey (ENSA 2000). Frequencies can be plotted onto a map on MexVar.
  • Human Genome Diversity Project (HGDP) 1k WGS – 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing (hg38 only).
  • Simons Genome Diversity Project (SGDP) 0.3k WGS – 279 whole genomes from 142 diverse and often indigenous populations worldwide, emphasizing anthropological, linguistic, and cultural diversity.
  • gnomAD HGDP+1000 Genomes 4k WGS – A reprocessed and harmonized callset of 4,094 whole genomes from 80 populations, combining the HGDP and 1000 Genomes datasets (hg38 only).

We would like to thank the Center for Research and Advanced Studies (Cinvestav) of Mexico, the Simons Foundation, David Reich and Swapan Mallick, and the Genome Aggregation Database Consortium (gnomAD) for making these data available. We would also like to thank Maximilian Haeussler and Jairo Navarro Gonzalez for creating and releasing these tracks.

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