Data/Code

Genomes Unzipped is a collaborative online project aiming to provide genetic testing customers with the knowledge and tools they need to make the most of their own genetic data. As part of the project our members are taking commercial genetic tests and making the raw data publicly available for others to download, analyse and reuse. There are currently three ways for users to access our genotype data.

1: Our Genome Browser

You can download our genotype data for particular parts of the genome, using the “Download Genotypes” link on the Genome Browser. Download genotype data for a particular SNP by clicking on it.

2: Download Complete Data

You can download all genotypes for particular individuals from our Amazon S3 genotype bucket, from the following locations:

23andMe v2 data:

• Daniel MacArthur (DGM001)
• Luke Jostins (LXJ001)
• Dan Vorhaus (DBV001)
• Caroline Wright (CFW001)
• Kate Morley (KIM001)
• Vincent Plagnol (VXP001)
• Jeff Barrett (JCB001)
• Jan Aerts (JXA001)
• Joe Pickrell (JKP001)
• Don Conrad (DFC001)
• Carl Anderson (CAA001)
• Ilana Fisher (IPF001)

23andMe v3 data:

• Daniel MacArthur (downloaded 19/02/11)

Lumigenix data:

• Daniel MacArthur (downloaded 13/04/11)

Counsyl reports:

• Counsyl report for DGM001 and IPF001.

If you want to download all of these files, use a download manager like DownThemAll, or using some S3 management software on the genotype bucket itself.

3: Use Our API

For more data-savvy users, we also have all the genotypes for GNZ participants stored in a database, that can be accessed using this genotype download script. The GET parameters are chr, start, end and id, only the first of which is required. start and end are chromosome positions on build 36 of the reference genome, and id is an rsID.

So, for instance, to look up rs490998 on chromosome 11, use

genomesunzipped.org/download/genotypes.php?chr=chr11&id=rs490998

or to download all SNPs between 1M and 2M on chromosome 2 use

genomesunzipped.org/download/genotypes.php?chr=chr2&start=1000000&end=2000000

You can also just pull out all SNPs on a chromosome by using just the chr argument; to get all mitochondrial variants, use

genomesunzipped.org/download/genotypes.php?chr=chrMT

All genotypes are relative to the forward strand on build 36.

Copyright

All data on this page are available under a Creative Commons 0 license, meaning they can be used for any purpose without restriction or attribution.

To the extent possible under law, Genomes Unzipped has waived all copyright and related or neighboring rights to Genomes Unzipped genotype data.

All other content on the Genomes Unzipped website, unless otherwise specified, is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported (CC BY-SA 3.0), and thus requires attribution if reused.

Code

All software that GNZ members produce as part of their analyses will be open source, and will be release via our GitHub repository. Descriptions and links will also be added to this page.

Delscan 0.1 – A program for identifying deletions using SNP genotype calls from parent-offspring trios. You can download the code here. This package contains binaries for some Mac OSX and Linux platforms. Windows users will need to compile separately. See README for usage and other details. Updates will be posted here periodically. Download delscan_0.1.tar.