SNV Frequencies Saudi Genome 302 WGS Track Settings
Version: SHGP (figshare 51297884, 2025) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
Variant frequencies from 302 whole genomes at 30x coverage from the
Saudi Genome Program. The genotyping data and imputations from 3,352
individuals do not seem to be available publicly.
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 saudi.
For bulk download, the VCF file can be obtained from
our download server.
The original data were downloaded from
Figshare and converted to VCF.
Methods
Whole-genome sequencing of 302 Saudi Arabian individuals was performed on the Illumina HiSeq
X Ten platform using TruSeq Nano DNA library preparation at 30x target coverage. Sequencing and
initial bioinformatics processing were carried out by deCODE Genetics (Reykjavík, Iceland).
Reads were aligned to the GRCh38 reference genome using BWA 0.7.10. Per-sample variants
were called with GATK HaplotypeCaller, then jointly genotyped with CombineGVCFs and
GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied for both SNPs and indels.
The final autosomal callset contains 25.5 million variants across the 302 individuals.
The variant data were downloaded from
Figshare and converted to VCF format using a custom script.
The makeDoc file documents how all source files of the varFreqs track were converted.
For some tracks, python scripts were needed; these are also available from GitHub.