Version: r1.1 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
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). After the lift
from GRCh37 to GRCh38, 38.3 million variants remain.
Data Access
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.
Methods
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.
The conversion steps for all source files of the varFreqs track are documented in the makeDoc file of the track.
Some tracks required python scripts, which are also available from GitHub.
Credits
Thanks to the Haplotype Reference Consortium and all contributing studies for making this
reference panel publicly available.