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Table 3 Summary of bioinformatics tools for CNV detection using exome 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.
Control-FREECa http://bioinfo-out.curie.fr/projects/freec/ C++ SAM/BAM/pileup/Eland, BED, SOAP, arachne, psi (BLAT) and Bowtie formats Correcting copy number using matched case-control samples or GC contents [53]
CoNIFERb http://conifer.sf.net/ Python BAM Using singular value decomposition to normalize copy number and avoiding batch bias by integrating multiple samples [54]
XHMMb http://atgu.mgh.harvard.edu/xhmm/ C++ BAM Uses principal component analysis to normalize copy number and HMM to detect CNVs [55]
ExomeCNVc http://cran.r-project.org/src/contrib/Archive/ExomeCNV/ R BAM/pileup Using read depth and B-allele frequencies from exome sequencing data to detect CNVs and LOHs [49]
CONTRAc http://contra-cnv.sourceforge.net/ Python SAM/BAM Comparing base-level log-ratios calculated from read depth between case and control samples [77]
CONDEX http://code.google.com/p/condr/ Java Sorted BED files Using HMM to identify CNVs [78]
SeqGene http://seqgene.sourceforge.net Python, R SAM/pileup Calling variants, including CNVs, from exome sequencing data [79]
PropSeqc http://bioinformatics.nki.nl/ocs/ R, C N/A Using the read depth of the case sample as a linear function of that of control sample to detect CNVs [52]
VarScan2c http://genome.wustl.edu/software/varscan Java BAM/pileup Using pairwise comparisons of the normalized read depth at each position to estimate CNV [50]
ExoCNVTestb http://www1.imperial.ac.uk/medicine/people/l.coin/ Java, R BAM Identifying and genotyping common CNVs associated with complex disease [56]
ExomeDepthb http://cran.r-project.org/web/packages/ExomeDepth/index.html R BAM Using beta-binomial model to fit read depth of WES data [30]
  1. aControl-FREEC accepts either matched case-control samples or single sample as input.
  2. bTools use multiple samples as input.
  3. cTools require matched case-control samples as input.