SegSeqa
|
http://www.broad.mit.edu/cancer/pub/solexa_copy_numbers/
|
Matlab
|
Aligned read positions
|
Detecting CNV breakpoints using massively parallel sequence data
|
[33]
|
CNV-seqa
|
http://tiger.dbs.nus.edu.sg/cnv-seq/
|
Perl, R
|
Aligned read positions
|
Identifying CNVs using the difference of observed copy number ratios
|
[31]
|
RDXplorerb
|
http://rdxplorer.sourceforge.net/
|
Python, Shell
|
BAM
|
Detecting CNVs through event-wise testing algorithm on normalized read depth of coverage
|
[28]
|
BIC-seqa
|
http://compbio.med.harvard.edu/Supplements/PNAS11.html
|
Perl, R
|
BAM
|
Using the Bayesian information criterion to detect CNVs based on uniquely mapped reads
|
[41]
|
CNAsega
|
http://www.compbio.group.cam.ac.uk/software/cnaseg
|
R
|
BAM
|
Using flowcell-to-flowcell variability in cancer and control samples to reduce false positives
|
[44]
|
cn.MOPSb
|
http://www.bioinf.jku.at/software/cnmops/
|
R
|
BAM/read count matrices
|
Modelling of read depths across samples at each genomic position using mixture Poisson model
|
[46]
|
JointSLMb
|
http://nar.oxfordjournals.org/content/suppl/2011/02/16/gkr068.DC1/JointSLM_R_Package.zip
|
R
|
SAM/BAM
|
Population-based approach to detect common CNVs using read depth data
|
[45]
|
ReadDepth
|
http://code.google.com/p/readdepth/
|
R
|
BED files
|
Using breakpoints to increase the resolution of CNV detection from low-coverage reads
|
[38]
|
rSW-seqa
|
http://compbio.med.harvard.edu/Supplements/BMCBioinfo10-2.html
|
C
|
Aligned read positions
|
Identifying CNVs by comparing matched tumor and control sample
|
[34]
|
CNVnator
|
http://sv.gersteinlab.org/
|
C++
|
BAM
|
Using mean-shift approach and performing multiple-bandwidth partitioning and GC correction
|
[40]
|
CNVnorma
|
http://www.precancer.leeds.ac.uk/cnanorm
|
R
|
Aligned read positions
|
Identifying contamination level with normal cells
|
[32]
|
CMDSb
|
https://dsgweb.wustl.edu/qunyuan/software/cmds
|
C, R
|
Aligned read positions
|
Discovering CNVs from multiple samples
|
[47]
|
mrCaNaVar
|
http://mrcanavar.sourceforge.net/
|
C
|
SAM
|
A tool to detect large segmental duplications and insertions
|
[35]
|
CNVeM
|
N/A
|
N/A
|
N/A
|
Predicting CNV breakpoints in base-pair resolution
|
[42]
|
cnvHMM
|
http://genome.wustl.edu/software/cnvhmm
|
C
|
Consensus sequence from SAMtools
|
Using HMM to detect CNV
|
N/A
|