A software tool for locating copy number variations using array CGH data

Chen, P.-A., Liu, H.-F., Chao, K.-M., 2008, "CNVDetector: Locating Copy Number Variations Using Array CGH Data", Bioinformatics, 24: 2773-2775.
CNVDetector is a program for locating copy number variations in a single genome using array CGH data. This program can detect the aberration regions in the array CGH data and output as a tabbing file. CNVDetector has several merits as follows.

CNVDetector is implemented in C++ and wxWidgets.
It is available as a Win32 executable:
Download CNVDetector v1.1 for Windows platforms (3.2mb)
The screenshot:

The three parameters in CNVDetector are described in the following:
The input file of CNVDetector is a tabbing text file with the following format:
FeatureNumber SymbolName Chromosome Position Sample1 Sample2
3334 GNB1 1 541338 -0.160 -0.450
32100 RER1 1 775446 1.01 0.823
Each column is separated by a tab; each row is sorted by the chromosome number first and then sorted by the position in the genome.
Field "Chromosome" contains one number from {1, 2, ..., 22}.

The Stepgram output format: this format can be easily plotted by Excel or other software tools.
ProbeID SymbolName Chromosome Position Level of Sample1 Level of Sample2
3334 GNB1 1 541338 -0.160 -0.450
32100 RER1 1 775446 0 0
Each column is separated by a tab.
The level of one probe equals to 0 represents that there are no copy number variations in this probe; otherwise it contains the log ratio of the corresponding probe.

Updated: 05/06/2008 09:10:30