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This wiki provides meta-instructions and help on using the internally-developed software of the Vertebrate Resequencing group at the Sanger Institute. We write and run software that tracks, processes and analyzes next-generation sequencing data.

vr-codebase is our main repository for all our pipelines and associated methods that do things like mapping, QC, SNP calling and so on.

The first thing you'll want to do is get a copy of our software. If you don't plan on developing our code and contributing improvements back to us, simply clone the repository and use the master branch. If you want to contribute, make your own fork of the repository and do your development on the develop branch before sending us a pull request. If you're new to git and preceding doesn't mean much to you, read our Using Git.