Birdsuite

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.

Papers

The paper (including supplement) detailing Birdsuite can be found on the Nature Genetics website, here:
 

 

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:
 

 

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

 

* For technical assisstance regarding the installation or running of Birdsuite, please contact the birdsuite help ticket system: birdsuite@broadinstitute.org