The Haplotype Reference Consortium (HRC) is a collaboration among several large sequencing projects to create a reference panel for genotype imputation. Release 1.1 contains 64,976 haplotypes from 32,488 whole-genome sequenced samples at low coverage (average 7x), with 40 million variant sites (minimum allele count of 5).
The contributing studies include the 1000 Genomes Project, UK10K, and many other cohorts. Since 1000 Genomes data is already available as a separate track, this track shows only the frequencies from the non-1000 Genomes samples (~30,000 individuals), resulting in 38.3 million variants after lifting from GRCh37 to GRCh38.
The data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, our REST API can be used; the track name is hrc. For bulk download, the VCF file can be obtained from our download server.
The original site list file can also be downloaded from the HRC website. Our GitHub repo contains a script that converts the tab-separated file to VCF and lifts it to hg38.
The HRC r1.1 site list was downloaded from the HRC website as a tab-separated file on GRCh37, converted to VCF and lifted to GRCh38 with UCSC liftOver. Only frequencies from the non-1000 Genomes samples (~30,000 of the 32,488 total) are included, since 1000 Genomes data is available separately. Of 40.4M input variants, 8,052 were unmapped by liftOver and 2.1M were present only in 1000 Genomes samples and were dropped, leaving 38.3M variants. We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. For some tracks, python scripts were necessary and are also available from GitHub.
Thanks to the Haplotype Reference Consortium and all contributing studies for making this reference panel publicly available.
McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet. 2016 Oct;48(10):1279-83. PMID: 27548312; PMC: PMC5388176