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Genome Aggregation Database (gnomAD) data are available at the links below. Please see this blog post for more information about this release.

Last updated October 3, 2017 11:29 AM: release gnomAD version 2.0.2.

Variant Dataset (VDS) format

Hail users can download gnomAD data in Variant Dataset (VDS) format.

First, install Google Cloud SDK. Then use the Google Cloud Storage gsutil tool to copy partitions in parallel to your own storage bucket or local hard drive. This blog post can help you get started with Hail on the cloud and this post shows you how to query variants by interval on your laptop.

mkdir gnomad_data

To download VDS files (note: autosomes are now combined with sex chromosomes):

gsutil -m cp -r gs://gnomad-public/release/2.0.2/vds/exomes/gnomad.exomes.r2.0.2.sites.vds gnomad_data # 16 GB
          gsutil -m cp -r gs://gnomad-public/release/2.0.2/vds/exomes/gnomad.exomes.r2.0.2.sites.split.vds gnomad_data
gsutil -m cp -r gs://gnomad-public/release/2.0.2/vds/genomes/gnomad.genomes.r2.0.2.sites.vds gnomad_data # 108 GB

The original ExAC dataset is available here:

gsutil -m cp -r gs://gnomad-public/legacy/exac_browser/ExAC.r1.sites.vds gnomad_data # 6.7 GB

VCF and coverage files

Files are linked in the table below, or you can explore the data directory here . To download multiple files in parallel on command line, follow these instructions:

First, install Google Cloud SDK (you will need a Google account). Then use the Google Cloud Storage gsutil tool to copy files in parallel to your own storage bucket or local hard drive. Here are some example commands for interacting with the storage bucket:

gsutil ls gs://gnomad-public/release/2.0.2
gsutil ls gs://gnomad-public/release/2.0.2/vcf/genomes

View file sizes:

gsutil du -h -s gs://gnomad-public/release/2.0.2/vcf/genomes # size of whole folder
gsutil du -h gs://gnomad-public/release/2.0.2/vcf/genomes # sizes of individual files

To download, find somewhere to put the data.

mkdir gnomad_data

Download all vcf files:

gsutil -m cp -r gs://gnomad-public/release/2.0.2/vcf gnomad_data # 102 GB

Or specific chromosomes:

# e.g. chromosome 1, 7 GB
gsutil -m cp -r gs://gnomad-public/release/2.0.2/vcf/genomes/gnomad.genomes.r2.0.2.sites.chr1.vcf.bgz gnomad_data