Interested in working on the development of this resource? Apply here.

Downloads

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

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 individual exome sites VDS files:

gsutil -m cp -r gs://gnomad-public/release-170228/gnomad.exomes.r2.0.1.sites.autosomes.vds gnomad_data # 16 GB
gsutil -m cp -r gs://gnomad-public/release-170228/gnomad.exomes.r2.0.1.sites.X.vds gnomad_data # 413 MB
gsutil -m cp -r gs://gnomad-public/release-170228/gnomad.exomes.r2.0.1.sites.Y.vds gnomad_data # 5 MB

To download individual genome sites VDS files:

gsutil -m cp -r gs://gnomad-public/release-170228/gnomad.genomes.r2.0.1.sites.autosomes.vds gnomad_data # 102 GB
gsutil -m cp -r gs://gnomad-public/release-170228/gnomad.genomes.r2.0.1.sites.X.vds gnomad_data # 5 GB

Or copy everything at once:

gsutil -m cp -r gs://gnomad-public/release-170228/* gnomad_data # 124 GB

VCF and coverage files

Update: March 3, 2017 8:18 AM. To increase download speed, we have made the VCF files available from Google Storage. The individual files are linked in the table below. To download multiple files in parallel on command line, follow these instructions (you will need a Google account):

First, install Google Cloud SDK. Then use the Google Cloud Storage gsutil tool to copy files in parallel to your own storage bucket or local hard drive. You can explore the data directory in a browser or on command line:

gsutil ls gs://gnomad-public/release-170228
gsutil ls gs://gnomad-public/release-170228/vcf/genomes

View file sizes, eg:

gsutil du -h -s gs://gnomad-public/release-170228/vcf/genomes # size of whole folder
gsutil du -h gs://gnomad-public/release-170228/vcf/genomes # sizes of individual files

To download, find somewhere to put the data.

mkdir gnomad_data

Download everything:

gsutil -m cp -r gs://gnomad-public/release-170228/vcf gnomad_data # 102 GB
gsutil -m cp -r gs://gnomad-public/release-170228/coverage gnomad_data # 1.8 GB

Or specific chromosomes:

# e.g. chromosome 1, 7 GB
gsutil -m cp -r gs://gnomad-public/release-170228/vcf/genomes/gnomad.genomes.r2.0.1.sites.1.vcf.gz gnomad_data