A software tool for locating copy number variations using array CGH data
References:
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.
- It can deal with the array CGH data even if the noise is not normally distributed.
- It requires less computation time.
- It evaluates the statistical significance for each aberration calling.
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:
- Threshold value affects the sensitivity of CNVDetector. It is usually set from
1.96 (95% confidence) to 3.89 (99.99% confidence).
More aberration callings are reported if the threshold value is set to a larger value.
- Length lower bound is the minimum number of probes that one CNV calling contains.
This number is usually set to 25.
- Length upper bound is the maximum number of probes that one CNV calling contains.
This number is set when we know the length upper limit of CNVs.
If the length upper limit is unknown, set this number to the maximum number of probes in one chromosome.
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}.
Testdata
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