Birdsuite
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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.
Project website: http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/birdsuite/birdsuite
An example job submission script can be found here (copy this to your job directory and make sure to edit the email address!)
/share/apps/example-scripts/birdsuite-job.qsub
Load SGE module
The following Modules files should be loaded for this package:
module load birdsuite/birdsuite-1.5