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 CNPs 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 Broad Institute, Cambridge, MA
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Joshua M Korn, Finny G Kuruvilla, Steven A McCarroll, Alec Wysoker, James Nemesh, Simon Cawley, Earl Hubbell, Jim Veitch, Patrick J Collins, Katayoon Darvishi, Charles Lee, Marcia M Nizzari, Stacey B Gabriel, Shaun Purcell, Mark Daly and David Altshuler
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs
Nature Genetics 40, 1253 – 1260 (2008) Published online: 7 September 2008 | doi:10.1038/ng.237