SNV Frequencies India IndiGenomes 1k WGS Track Settings
Version: IndiGen pilot (Jain 2021) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
IndiGenomes provides
whole genome sequencing data of 1,029 healthy Indian individuals under the pilot phase of the
"IndiGen" program. The IndiGenomes website also provides SV call and Alu insertion VCFs.
The deployed VCF shown in this track is the public release subset distributed by the
IndiGenomes project (18,016,257 records). The full Jain 2021 callset reports 55.8 million
variants from the 1,029-genome cohort; the public release is a curated subset of those
sites. The deployed VCF is sites-only and carries a per-variant VRT (variant type)
INFO field. Per-variant allele counts and allele frequencies are not distributed with the
public release and are not shown in this track.
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 indigenomes.
For bulk download, the VCF file can be obtained from
our download server.
The original data can also be downloaded from the IndiGen website.
Methods
Genomic DNA was extracted from 5 ml of peripheral blood collected via venipuncture from
1,029 self-declared healthy Indian individuals representing diverse geographic, ethnic, and
linguistic groups, using the salting-out method. Whole-genome libraries were prepared using
the TruSeq DNA PCR-free library preparation kit (Illumina). Sequencing was performed on the
Illumina NovaSeq 6000 platform with 150×2 bp paired-end reads targeting ≥30×
mean coverage. Alignment to the GRCh38 reference genome, post-processing, and
default quality-filtered variant calling were performed end-to-end on the Illumina DRAGEN
v3.4 Bio-IT platform, which uses field-programmable gate array (FPGA) logic for
high-throughput processing. The full Jain 2021 callset comprises 55,898,122 single-allelic
genetic variants (SNVs and indels), of which 32.23% were unique to the Indian samples
and absent from global reference databases. Variants were annotated using ANNOVAR with
RefGene, and allele frequencies were cross-referenced against gnomAD v3, 1000 Genomes,
ExAC, ESP6500, and the Greater Middle East Variome Project. The
IndiGenomes database
distributes a public-release subset of these variants (18,016,257 records); that subset is
the file used in this track.
(Jain, Bhoyar, Scaria, Sivasubbu & the IndiGen Consortium,
Nucleic Acids Research 2021).
The makeDoc file of the track documents how all source files of the varFreqs track were converted.
For some tracks, python scripts were also used and are available from GitHub.