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Table 2 Read depth (RD)-based tools for CNV detection using whole genome sequencing data

From: Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

Tool URL Language Input Comments Ref.
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
  1. aTools require matched case-control sample as input.
  2. bTools use multiple samples as input.