Version: Pilot 2019 (lifted to hg38, May 2026) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
The GenomeAsia 100K project aims
to sequence 100,000 Asian individuals. This pilot release (GAsP) contains whole-genome sequencing
data of 1,739 individuals from 219 population groups across Asia. Frequencies are broken down by
Northeast Asian, Southeast Asian, and South Asian ancestry groups. The data is split into two
subtracks: substitutions and indels.
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 gasp.
For bulk download, the VCF file can be obtained from
our download server.
The original VCFs are also available from the
GenomeAsia 100K
website. No license nor login is required.
Methods
Samples were sequenced on Illumina HiSeq 2500, HiSeq 4000, and HiSeq X Ten instruments with
2×100 bp or 2×150 bp paired-end reads at an average depth of 36x. Reads were aligned to
GRCh37 using BWA-MEM. Duplicate reads were marked with SAMBLASTER and sorted with Sambamba.
Per-sample variant calling was performed with GATK HaplotypeCaller in GVCF mode, followed by
joint genotyping with GenotypeGVCFs. Variant quality score recalibration (VQSR) was applied at
a 99% sensitivity tranche for both SNPs and indels. Sample-level QC included contamination
checks with verifyBamID and sex concordance verification. The final callset contains
∼65 million variants across 1,739 individuals from 219 populations.
The upstream callset is on GRCh37. We lifted it to hg38 using
CrossMap and the UCSC
hg19ToHg38 chain file. After lifting, variants that landed on alt, random, fix, or
unplaced contigs were dropped, and the result was sorted and indexed with tabix.
The makeDoc file documents how all source files of the varFreqs track were converted.
For some tracks, python scripts were needed and are also available from GitHub.