Table 4 Combinatorial bioinformatics tools for CNV detection using NGS data

NovelSeq

http://compbio.cs.sfu.ca/strvar.htm

C

FASTA/SAM

PEM+AS

[66]

HYDRA

http://code.google.com/p/hydra-sv/

Python

Discordant paired-end mappings

PEM+AS

[67]

CNVer

http://compbio.cs.toronto.edu/CNVer/

Perl, C++

BAM/aligned positions

PEM+RD

[61]

GASVPro

http://code.google.com/p/gasv/

C++

BAM

PEM+RD

[63]

Genome STRiP

http://www.broadinstitute.org/software/genomestrip/genome-strip

Java, R

BAM

PEM+RD

[62]

SVDetect

http://svdetect.sourceforge.net/

Perl

SAM/BAM/ELAND

PEM+RD

[60]

inGAP-sv

http://ingap.sourceforge.net/

Java

SAM

PEM+RD

[64]

SVseq

http://www.engr.uconn.edu/~jiz08001/svseq.html

C

FASTQ/BAM

PEM+SR

[73]

Nord et al.

N/A

N/A

N/A

RD+SR

[74]