IndiGenomes provides whole genome sequencing data of 1,029 healthy Indian individuals under the pilot phase of the -"IndiGen" program. Only the allele frequency is available from this project. The website -also provides SV call and Alu insertion VCFs. +"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 therefore are not shown in this track.
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.
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. This yielded a compendium of 55,898,122 single allelic +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 dataset is accessible via -the IndiGenomes database +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).
We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. For some tracks, python scripts were necessary and are also available from GitHub.
Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B et al. IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes. Nucleic Acids Res. 2021 Jan 8;49(D1):D1225-D1232. PMID: 33095885; PMC: PMC7778947