Table 3 Computational tools for cancer genomics

Alignment

MAQ

http://maq.sourceforge.net/

[34]

BWA

http://bio-bwa.sourceforge.net/

[35, 36]

Bowtie2

http://bowtie-bio.sourceforge.net/bowtie2/

[37]

BFAST

http://bfast.sourceforge.net

[38]

SOAP2

http://soap.genomics.org.cn/soapaligner.html

[39]

Novoalign/NovoalignCS

http://www.novocraft.com/

SSAHA2

http://www.sanger.ac.uk/resources/software/ssaha2/

[40]

SHRiMP

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

[41]

Mutation calling

GATK

http://www.broadinstitute.org/gatk/

[42]

Samtools

http://samtools.sourceforge.net/

[43]

SOAPsnp

http://soap.genomics.org.cn/soapsnp.html

[44]

SNVmix

http://compbio.bccrc.ca/software/snvmix/

[45]

VarScan

http://varscan.sourceforge.net/

[46, 50]

Somaticsniper

http://gmt.genome.wustl.edu/somatic-sniper/

[51]

JointSNVMix

http://compbio.bccrc.ca/software/jointsnvmix/

[52]

SV detection

BreakDancer

http://breakdancer.sourceforge.net/

[57]

VariationHunter

http://variationhunter.sourceforge.net/

[58]

PEMer

http://sv.gersteinlab.org/pemer/

[59]

SVDetect

http://svdetect.sourceforge.net/

[60]

Function effect of mutation

SIFT

http://sift.jcvi.org/

[53]

CHASM

http://wiki.chasmsoftware.org

[55]

PolyPhen-2

http://genetics.bwh.harvard.edu/pph2/

[54]

ANNOVAR

http://www.openbioinformatics.org/annovar/

[56]