PennCNV main package

The link to latest stable version of PennCNV main package is given below. The package includes both source codes and pre-compiled executables for Windows. (Due to the problem of several unzipping software under Windows in handling *.tar.gz files, Windows users should try to download the zip file instead. The contents of these two files are identical).

Alternatively, users can download the cutting edge version from GitHub by git clone

User-supplied files and programs

Users can use the program included in PennCNV to generate a PFB file for their specific arrays. A few additional PFB files are provided below:

A few user contributed programs/scripts are provided below:

PennCNV example data sets

This example data set contains genotyping data for a father-mother-offspring trio, genotyped on the Illumina HumanHap550 array. The file is in BeadStudio project format, and can be opened by the Illumina BeadStudio software. The file is used in the tutorial in the web site.

This file is an exported text file from the Illumina BeadStudio software using the above project file. It is useful for users without access to BeadStudio to test PennCNV.

This serial dilution data set contains genotyping data on a sample genotyped five times, each time with ~2-fold dilutions. For more details please see the Diskin et al paper. The file is in BeadStudio project format, and can be opened by the Illumina BeadStudio software.

PennCNV-Affy protocols

This package contains PennCNV-Affy protocols and helper scripts for handling Affymetrix Mapping 500K, genome-wide 5.0 and genome-wide 6.0 data as raw CEL files. For instructions on how to use the PennCNV-Affy package, please refer to the PennCNV-Affy link in the menu bar to the left of the page. The package below is updated on 2009Aug27, with very minor bug fixes only. It should produce identical results as previous version.

Genome Browser tracks for SNP arrays

Click any of the link below will load the corresponding track in the UCSC Genome Browser on hg18 coordinate, or 2006 human genome assembly. It may take several minutes to load each of the track. The user can visualize the location of the marker coverage in each specific arrays and compare them with each other. If the user does not want to see the marker names in the browser, the dense drop-down menu option can be used in the browser page to display red vertical bars for each marker.

All the genome coordinates are also annotated in the PFB file supplied with the PennCNV package. The Illumina data were based on supplied annotation from Illumina's sample files. The Affymetrix data were based on na26 (July 2008) annotation from Affymetrix website.

Please report annotation mistakes/bugs or request for additional arrays.