Birdsuite

The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Variants (CNVs), and rare/de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to simply do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

Authors: Joshua Korn^1,2,3, Finny Kuruvilla^1,4,5, Steven McCarroll^1,5, Alec Wysoker¹, Jim Nemesh¹, Marcia Nizzari¹, Stacey Gabriel¹, Mark Daly^1,6, and David Altshuler^1,5,6

Affiliations: 1. The Broad Institute of Harvard and MIT 2. Department of Biophysics, Harvard University 3. Harvard-MIT Division of Health Sciences and Technology 4. Department of Pathology, Brigham & Women's Hospital 5. Department of Molecular Biology, Massachusetts General Hospital 6. Center for Human Genetic Research, Massachusetts General Hospital

Development of the SNP5.0 and SNP6.0 platforms, as well as associated algorithms, have been a collaboration with Affymetrix, Inc.

Overview

• A high-level description of the Birdsuite and its components

Download

• Download the actual Birdsuite, or just the auxillary files for Birdseed

Install

• Installation information

How-to

• A guide to running the Birdsuite

Support

• gap-support@broad.mit.edu