SNV Frequencies UK Biobank 361k imputed Track Settings
Version: Neale Lab R2 08-2018 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
This track shows allele frequencies and imputation quality scores for
13,743,085 variants observed in 361,194 UK Biobank participants of white
British ancestry. The
UK Biobank
is a prospective study of around 500,000 adults aged 40-69 at recruitment
in the UK, with linked genotype, imaging and health-record data. The
allele counts shown here are taken from the Neale Lab's open release of
imputed-v3 GWAS results, which the Lab made freely available as a
companion to their large phenotype-wide GWAS of UK Biobank (Round 2 of
the
Neale Lab
UK Biobank GWAS).
The Neale Lab pipeline restricts to white British ancestry to limit
population-stratification confounding in the GWAS. As a consequence the
frequencies in this track are not representative of the multi-ancestry UK
Biobank cohort. They describe a single population subset. The
gnomAD HGDP+1kG,
ToMMo Japan,
AllOfUs and other tracks in this
collection provide complementary frequencies from other populations.
Display
The track uses the standard UCSC VCF display. Hover over a variant to see
the allele frequency, imputation INFO score, HWE p-value, hom-ref / het /
hom-alt sample counts and the most-severe VEP consequence reported by
the Neale Lab.
Methods
UK Biobank participants were genotyped on the UK Biobank Axiom and UK
BiLEVE Axiom arrays. The Wellcome Trust Centre for Human Genetics imputed
the array data against a combined reference panel of the Haplotype
Reference Consortium, UK10K and 1000 Genomes Phase 3. This produced
approximately 90 million imputed SNPs. The Neale Lab Round 2 (imputed-v3)
analysis started from the 487,409 individuals with phased and imputed
genotype data, filtered to 361,194 unrelated samples of white British
ancestry, and retained variants with imputation INFO score above 0.8,
minor allele frequency above 0.001 (or 1e-6 for coding variants) and
HWE p-value above 1e-10. The final set has 13.7 million SNPs and short
indels on chromosomes 1-22 and X. Variant consequences are from Ensembl VEP. See
the Neale Lab
data
processing blog post and the
UK_Biobank_GWAS
GitHub repository for the full pipeline.
The variant manifest
variants.tsv.bgz was downloaded from the Neale Lab
UK Biobank
GWAS results page. The Neale Lab release uses GRCh37 coordinates and
provides chromosome, position, reference and alternate alleles, dbSNP
rsID, VEP consequence, imputation INFO score, allele count and
frequency, Hardy-Weinberg p-value and per-genotype sample counts. We
converted the TSV to a sites-only VCF using a custom Python script and
lifted the coordinates to GRCh38 with CrossMap and the UCSC
hg19ToHg38.over.chain. 39,659 rows with allele count zero (variants
present only in the imputation panel) were dropped, 6,889 failed
liftOver and 1,834 mapped to alt/random/fix contigs, leaving 13,743,085
variants in the final file. AN was set to twice the
n_called field, per the Neale Lab convention.
The full pipeline is documented in the
makeDoc
file of the track, and the conversion script is available from
our
GitHub repository.
Data Access
The variant frequencies can be explored with the
Table Browser or the
Data Integrator, and exported to
spreadsheet or tab-separated tables. From scripts, data can be accessed
via our REST API
with track=ukbb.
The VCF file is also available from
our
download server as ukbb.vcf.gz. Individual regions can be
extracted with tabix, for example
tabix http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/ukbb/ukbb.vcf.gz chr21:1-100000000.
The original Neale Lab manifest variants.tsv.bgz is linked from
the
Neale Lab UK
Biobank GWAS results page and is distributed under UK Biobank's
data-access conditions.
Credits
Thanks to the UK Biobank participants and to Benjamin Neale, Liam
Abbott, Raymond Walters, Duncan Palmer and the rest of the Neale Lab for
making the Round 2 imputed-v3 GWAS results, including the variant
manifest used here, publicly available.