SNV Frequencies China ChinaMAP 10.5k WGS Track Settings
Version: Phase 1 (v2020-03.beta) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
This track shows allele frequencies for 147.4 million variants (136.7
million SNPs and 10.7 million short indels, autosomes only) from
10,588 Chinese individuals deep-whole-genome-sequenced at a mean depth
of about 40x by the China Metabolic Analytics Project (ChinaMAP).
Participants come from three large Chinese cohort studies (the China
Noncommunicable Disease Surveillance, the REACTION study and the
Community-based Cardiovascular Risk During Urbanization in Shanghai
study) and span 27 provinces of China and eight ethnic populations
(Han, Hui, Manchu, Miao, Mongolian, Yi, Tibetan and Zhuang). For
each variant the track records the cohort allele count, allele number
and allele frequency. The original release also ships the matched 1000
Genomes Project (1KGP) allele frequencies (global, EAS, AMR, AFR, EUR
and SAS) as INFO fields, which are kept verbatim in the VCF.
Display
The track uses the standard UCSC VCF display. When you hover over a
variant, the popup shows the cohort allele frequency and count, the
total number of called alleles, and the 1KGP frequencies that the
ChinaMAP release ships alongside each site.
Methods
DNA from each participant was prepared with the QIAGEN DNeasy
Blood & Tissue Kit, sheared by Covaris, ligated to BGISEQ-500
adapters and rolling-circle amplified into DNA nanoballs for
100 bp paired-end sequencing on the BGISEQ-500 platform at BGI
Genomics. Reads were quality-filtered with SOAPnuke v1.5.6, aligned
to GRCh38 (GENCODE release) with BWA-MEM v0.7.16a, coordinate-sorted
with Picard SortSam v2.13.2, and duplicate-marked and base-quality
recalibrated with GATK v4.beta.4. Samples were required to pass six
QC criteria (base quality Q30 > 80%, mean depth > 30x, mapping
rate ≥ 95%, mismatch rate < 1%, duplicate rate < 10% and
20x coverage > 80%) and a 21-SNP mass spectrometric fingerprint
check; 10,588 WGS samples passed. Germline variants were called
per-sample as GVCFs with GATK HaplotypeCaller v4.0.4.0, combined
with GATK CombineGVCFs and joint-called with GATK GenotypeGVCFs
(v4.0.4.0), ignoring low-complexity regions. Variants were filtered
with GATK VariantFiltration and restricted to length ≤ 10 bp and a
maximum of 10 alt alleles. Multi-allelic sites were split, and the
final callset was annotated with SnpEff v4.3. See Cao et al.
2020 (in References below) for the full pipeline.
The bgzipped sites-only VCF
(mbiobank_ChinaMAP.phase1.vcf.gz) was downloaded from the
ChinaMAP / mBiobank distribution site
(http://chinamapwgs.mbiobank.com/download/),
renamed locally to chinamap.vcf.gz and tabix-indexed. We did
not need to lift over coordinates or reformat the file: the upstream
file is already on GRCh38 with chr-prefixed chromosome names,
autosomes only, and ships standard AC, AF and
AN INFO fields. The pipeline is recorded in the
makeDoc
file of the track.
Caveats
Only autosomes (chr1-22) are present; chrX, chrY and chrM are not
in the ChinaMAP phase 1 release. The 1KGP frequency fields
(1KGP_AF, 1KGP_EAS_AF, 1KGP_AMR_AF,
1KGP_AFR_AF, 1KGP_EUR_AF, 1KGP_SAS_AF) are
carried over verbatim from the ChinaMAP VCF and only populate the
small fraction of ChinaMAP sites that are also catalogued in the
matched 1KGP release.
Data Access
The ChinaMAP Limitations on Use (see the
ChinaMAP
download page) prohibit redistribution of the data, so the
ChinaMAP VCF is not available from the UCSC Table Browser, Data
Integrator, REST API or the public download server. The track can be
browsed interactively in the Genome Browser; for bulk access please
register with the ChinaMAP project at
http://chinamapwgs.mbiobank.com/
and download the original VCF directly from them.
Credits
Thanks to the ChinaMAP participants and to the National Clinical
Research Center for Metabolic Diseases (Shanghai Jiao Tong
University School of Medicine, Ruijin Hospital) and BGI Genomics, who
produced and released the ChinaMAP phase 1 sites VCF.