CBS (v3)

Segments DNA copy number data into regions of estimated equal copy number using circular binary segmentation (CBS).

Author: Adam Olshen (UCSF)

Contact:

gp-help@broadinstitute.org

Algorithm Version:

Summary

Segments copy number data using the methodology described in Olshen et. al., 2004.

References

  1. Olshen, A. B., Venkatraman, E. S., Lucito, R., and Wigler, M. (2004). Circular binary segmentation for the analysis of array-based dna copy number data. Biostatistics, 5:557–72. Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W. L., Chen, C., Zhai, Y., Dairkee, S. H., Ljung, B. M., Gray, J. W., and Albertson, D. G. (1998). High resolution analysis of dna copy number variation using comparative genomic hybridization to microar- rays. Nat. Genet., 20:207–211.
  2. Lucito, R., Healey, J., Alexander, J., Reiner, A., Esposito, D., Chi, M., Rodgers, L., Brady, A., Sebat, J., Troge, J., West, J., Rostan, S., Nguyen, K., Powers, S., Ye, K., Olshen, A., Venkatraman, E., Norton, L., and Wigler, M. (2003). Representational oligonucleotide microarray analysis: a high resolution method to detect genome copy number variation. Nat. Genet., 13:2291–305.
  3. Snijders, A. M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A. K., Huey, B., Kimura, K., S, S. L., Myambo, K., Palmer, J., Ylstra, B., Yue, J. P., Gray, J. W., Jain, A. N., Pinkel, D., and Albertson, D. G. (2001). Assembly of microarrays for genome-wide measurement of dna copy number. Nat. Genet., 29:263–4. Venkatraman, E. S. and Olshen, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array cgh data. Bioinformatics, 23:657–63. 

Parameters

Name Description
input file * Copy number file - .cn
sample name  The name of the sample to use. Leave blank to use the first sample in the input file.
permutations * Number of permutations used for p-value computation
significance level * Significance levels for the test to accept change-points
output prefix * The prefix to use for the output file name

* - required

Input Files

  1. <input.file>
    Copy number file in *.cn format.

Output Files

  1. *.cbs.txt
    A tab delimited text file with six columns: the sample id, the chromosome number, the map position of the start of the segment, the map position of the end of the segment, the number of markers in the segment, and the average value in the segment.

 

Platform Dependencies

Task Type:
SNP Analysis

CPU Type:
any

Operating System:
any

Language:
R-2.15.3

Version Comments

Version Release Date Description
3 2015-12-02 Updated to use R-2.15 and the new package installer mechanism, and to add HTML documentation.
2 2012-09-07 Updated to use R package DNAcopy v1.28.0 Modified to only run one sample at a time. See ParallelCBS Pipeline documentation for running multiple samples in parallel.
1 2010-03-19