The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or 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 only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs. Support for chips and platforms other than the Affymetrix SNP 6.0 is currently limited, but we are currently working on creating the supporting files for other common genotyping platforms.

The paper (including supplement) detailing Birdsuite can be found on the Nature Genetics website, here:
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
A related paper that is important background reading for the design of SNP-CNV hybrid arrays and CNV properties can be found in the same issue of Nature Genetics, here:
Integrated detection and population-genetic analysis of SNPs and copy number variation

Authors: Joshua M Korn1-5, Finny G Kuruvilla1,4-6, Steven A McCarroll1,4,5, Alec Wysoker1, James Nemesh1, Simon Cawley7, Earl Hubbell7, Jim Veitch7, Patrick J Collins7, Katayoon Darvishi8, Charles Lee8, Marcia M Nizzari1, Stacey B Gabriel1, Shaun Purcell1,5, Mark Daly1,5,9, and David Altshuler1,4,5,9

Affiliations: 1. The Broad Institute of Harvard and MIT 2. Harvard-MIT Division of Health Sciences and Technology (HST) 3. Graduate Program in Biophysics, Harvard University 4. Department of Molecular Biology, Massachusetts General Hospital 5. Center for Human Genetic Research, Massachusetts General Hospital 6. Department of Pathology, Brigham and Women's Hospital 7. Affymetrix, Inc. 8. Department of Pathology, Harvard Medical School 9. Department of Medicine, Harvard Medical School


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


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


  • Installation information


  • A guide to running the Birdsuite

Analyzing Birdsuite output

  • How to work with the output of Birdsuite


  • For technical assisstance regarding the installation or running of Birdsuite, please contact the Broad Genotyping Analysis Platform:
  • For questions regarding the methdology, or how to use the output, please contact Joshua Korn:
  • For questions on using Birdsuite output in PLINK, please see the PLINK webpage, specifically sections 21 (Rare CNVs) and 22 (Common CNPs):
    PLINK homepage