Download the latest version of CoNIFER using the following link:

CoNIFER Python Files Version 0.2.2; Released 9/17/2012

Older version of CoNIFER will be available available here.

The sample data set of 26 RPKM files (listed below) can be downloaded here:

Sample RPKM Files

Study	Exome Capture	N	Samples
HapMap	Nimblegen V1 (2009)	8	NA12878, NA15510, NA18507, NA18517, NA18555, NA18956, NA19129, NA19240
Autism Trios	Nimblegen V2 (2010)	18	6 Trios (Mother, Father, Proband)

CoNIFER is implemented as a set of python scripts. In order to run CoNIFER, you need Python 2.7 or later, as well as the following python modules:

Package		Description
NumPy	Required	Array and SVD methods
PyTables	Required	File handling and storage
pysam	Optional	Needed only to create read-depth files from BAM files
matplotlib	Optional	Used for plotting images of calls, etc.