Downloading CoNIFER:

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.

Other files:

The sample data set of 26 RPKM files (listed below) can be downloaded here:
Sample RPKM Files
StudyExome CaptureNSamples
HapMapNimblegen V1 (2009)8NA12878, NA15510, NA18507, NA18517, NA18555, NA18956, NA19129, NA19240
Autism TriosNimblegen V2 (2010)186 Trios (Mother, Father, Proband)

Other Requirements:

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:
NumPyRequiredArray and SVD methods
PyTablesRequiredFile handling and storage
pysamOptionalNeeded only to create read-depth files from BAM files
matplotlibOptionalUsed for plotting images of calls, etc.