SNV Frequencies China WBBC 4.5k WGS Track Settings
Version: Phase I v20210103 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
This track shows allele frequencies for 78.6 million variants from
4,480 whole-genome-sequenced Chinese individuals released by the
Westlake BioBank for Chinese
(WBBC) pilot project. The WBBC is a population study of about 35,000
Chinese volunteers across 31 provinces; about 15,000 have been deeply
phenotyped and a subset have been whole-genome sequenced.
The frequencies are also broken down into four Han Chinese regional
groups (North, Central, South, Lingnan) defined by recruitment province
in the WBBC paper.
The pilot project has been folded into the larger
China Precision BioBank
(CPBB) initiative, which is collecting up to 100,000 samples
nationwide. The variant frequencies on this track are from the original
WBBC Phase I release (v20210103) and are unchanged by the rebranding.
Display
The track uses the standard UCSC VCF display. Hovering a variant shows
the cohort allele frequency, the four regional frequencies, sequencing
depth, GATK VQSR log-odds score, and the per-genotype hom-ref / het /
hom-alt sample counts as reported by WBBC.
Methods
The WBBC pilot whole-genome-sequenced 4,535 individuals at a mean depth
of 13.9x on Illumina HiSeq X10 platforms, after dropping samples that
failed standard QC. Reads were aligned to GRCh38 with BWA-MEM, variants
were jointly called with GATK 4.0 HaplotypeCaller, and the callset was
hard-filtered with VQSR. The 4,480 unrelated samples released for download
were stratified into four Han Chinese regional groups (North, Central,
South and Lingnan, which together cover 27 of the administrative divisions
the pilot reached). Allele counts and frequencies are reported overall
and per region. See Cong et al. 2022 (in References below) for
full sample-selection and pipeline details.
The per-chromosome WGS sites VCFs (chr1-22) were downloaded from
https://wbbc.westlake.edu.cn/
(URL pattern: WBBC.chr<N>.GRCh38.vcf.gz). We concatenated
the 22 files with bcftools concat, re-headered the result to
add the standard hg38 contig lines and proper INFO definitions, then
dropped variants with cohort allele count zero (multi-allelic splits
that no WBBC sample carries; ~1.9% of rows), and sorted, bgzipped and
tabix-indexed the result. No coordinate liftover was
needed: the upstream files are already on GRCh38 with chr-prefixed
chromosomes. The pipeline is recorded in the
makeDoc
file of the track.
Caveats
Only autosomes (chr1-22) are present; chrX/Y/M are not in the WBBC
download. Variants reported as AC=0 in the WBBC release (about 1.9 %
of rows, mostly multi-allelic split sites that no WBBC individual
carries) have been removed from this track.
Data Access
The variant frequencies can be explored interactively using the
Table Browser or the
Data Integrator, and exported to
spreadsheet or tab-separated tables. From scripts, the data can be
accessed via our REST
API with track=wbbc.
The VCF file is also available from
our
download server as wbbc.vcf.gz. Individual regions can be
extracted with tabix, for example
tabix http://hgdownload.soe.ucsc.edu/gbdb/hg38/varFreqs/wbbc/wbbc.vcf.gz chr21:1-100000000.
The original per-chromosome WBBC release is distributed at
https://wbbc.westlake.edu.cn/.
Credits
Thanks to the WBBC participants and to the Westlake University team
(Pei-Kuan Cong, Hou-Feng Zheng and colleagues) for making the pilot
sites-only VCFs publicly available.