gnomAD Allele frequency

The Genome Aggregation Database (gnomAD) is a critical resource for genetic studies, providing a high-precision frequency map of human genetic variations. The latest release, gnomAD v4.1, incorporates sequencing data from 807,162 individuals, a fivefold increase compared to previous versions. It includes two core datasets:

1. Exome Dataset: Covers 730,947 individuals, including 416,555 samples from the UK Biobank.
2. Whole Genome Dataset: Includes 76,215 individuals with whole-genome sequencing data.

All data are based on the Hg38 reference genome and integrate resources from projects like ExAC, 1000 Genomes, and UK Biobank. A standardized QC pipeline ensures data reliability by filtering low-quality samples and variants.

KGGA has extracted three distinct datasets from gnomAD v4.1: the whole-genome sequencing frequency data, the exome sequencing frequency data, and the joint dataset. These datasets provide comprehensive mutation frequency information across global populations, serving as a critical resource for disease association studies.

Generate gnomAD Annotation Files

1. Switch to the gnomAD directory:

cd path/to/gnomad/vcf/files

1. Run the command to generate the annotation file:

java -Dccf.compressor.zstd.level=16 -jar kgga.jar gbc make-database --gnomad $(echo $(ls *.vcf.bgz) | tr ' ' ',') -o gnomad.joint.v4.1.sites.hg38.gtb -t 20

Command Explanation

gnomAD Annotation Fields