Version: r5.3.2 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
The National Precision Medicine (NPM) program
in Singapore sequenced 9,770 whole genomes, mostly of Chinese, Indian and Malay ancestry.
A minimum allele count cutoff of >5 was applied. CNV data is also available.
Data Access
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
Whole Genome Sequencing (WGS) data processing followed GATK4 best practices. The GATK4 germline
variant analysis workflow written in WDL was adapted to Nextflow and deployed at the National
Supercomputing Centre, Singapore (NSCC). WGS reads were aligned against GRCh38 with the BWA-MEM
algorithm and used as input to GATK HaplotypeCaller to produce single sample gVCFs. The gVCF files
were joint-called then loaded in Hail. Low-quality WGS libraries and low-quality variants were
removed. QC-ed variants were functionally annotated with Ensembl Variant Effect Predictor (VEP)
(version 95). For variants that affect protein-coding regions, the annotations also include
information on potential changes to the cognate protein's 3D structure and drug binding ability.
Our data access request was approved by the NPM data access committee. It can be contacted at contact_npco@a-star.edu.sg.
We downloaded the data from the NPM Chorus browser download section.
The makeDoc file of the track documents how all source files of the varFreqs track were converted.
For some tracks, python scripts were necessary and are also available from GitHub.
Credits
Thanks to the NPM Data Access Committee and Eleanor for granting our data request.
By browsing the data, you agree to use the data only for academic, non-commercial
research to improve human health (biology/disease). We request all data users
agree to protect the confidentiality of the data subjects in any research papers or publications
that they may prepare, by taking all reasonable care to limit the possibility
of identification. In particular, the data users shall not use, or attempt
to use, the data to deliberately compromise or otherwise infringe the
confidentiality of information on data subjects and their right to privacy.
If you use any of the data obtained from the CHORUS variant browser, we request
that you cite the NPM flagship paper (Wong et al, 2023). All data users of the
data must take note that the data provider and relevant SG10K_Health cohort
owners bear no responsibility for the further analysis or interpretation of the data.