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. Author manuscript; available in PMC: 2011 Apr 13.
Published in final edited form as: J Genet Genomics. 2011 Mar 15;38(3):95–109. doi: 10.1016/j.jgg.2011.02.003

Table 4.

The genetic variant prediction and detection bioinformatic programs for NGS data analysis.

Variant prediction/detection Platform Website
Functional variant prediction
B-SIFT http://research-pub.gene.com/bsift/
MAPP http://mendel.stanford.edu/supplementarydata/stone_MAPP_2005
PhD-SNP http://gpcr.biocomp.unibo.it/~emidio/PhD-SNP/PhD-SNP
PolyPhen-2/PolyPhen http://genetics.bwh.harvard.edu/pph2/
SIFT http://blocks.fhcrc.org/sift/SIFT.html
SNAP http://www.rostlab.org/services/SNAP
SNAPper/Pedant http://pedant.gsf.de/snapper
Variant detection
Structural/genomic variant
BreakDancer Roche/Illumina/ABI http://genome.wustl.edu/tools/cancer-genomics/
BreakDancer/BD- Mini Roche/Illumina/ABI http://seqanswers.com/wiki/BreakDancer
Breakway Roche/Illumina/ABI http://sourceforge.net/projects/breakway/files/
CNVSeq Roche http://tiger.dbs.nus.edu.sg/CNV-seq/
cnvHMM Illumina http://genome.wustl.edu/pub/software/cancer-genomics/cnvHMM/
cnD Illumina http://www.sanger.ac.uk/resources/software/cnd.html
GASV/GSV Illumina http://cs.brown.edu/people/braphael/software.html
Hydra Illumina http://code.google.com/p/hydra-sv/
MoDIL Illumina http://compbio.cs.toronto.edu/modil/
mrFAST Illumina http://mrfast.sourceforge.net/
NovelSeq Roche/Illumina/ABI http://compbio.cs.sfu.ca/strvar.htm
PEMer Roche/Illumina/ABI http://sv.gersteinlab.org/pemer/
Pindel Illumina http://www.ebi.ac.uk/~kye/pindel/
SegSeq Illumina/ABI http://www.broadinstitute.org/
SOAPsv Roche/Illumina/ABI http://soap.genomics.org.cn
Solid large Indel tool ABI http://solidsoftwaretools.com/gf/project/large_indel/
Solid CNV tool ABI http://solidsoftwaretools.com/gf/project/cnv/
SWT Illumina http://genome.wustl.edu/pub/software/cancer-genomics/GSTAT/
VariationHunter/VH-CR Illumina http://compbio.cs.sfu.ca/strvar.html
VARiD ABI http://compbio.cs.utoronto.ca/varid
Single nucleotide variant
Atlas-SNP2 Roche/Illumina http://www.hgsc.bcm.tmc.edu/cascade-tech-software-ti.hgsc
BOAT Illumina http://boat.cbi.pku.edu.cn/
DNA Baser Roche http://www.dnabaser.com/help/manual.html
DNAA Roche/Illumina/ABI http://sourceforge.net/projects/dnaa/
Galign Illumina http://shahamlab.rockefeller.edu/galign/galign.htm
GigaBayes/PbShort Roche/Illumina http://bioinformatics.bc.edu/marthlab/GigaBayes
GSNAP Roche/Illumina http://share.gene.com/gmap.
inGAP Roche/Illumina http://sites.google.com/site/nextgengenomics/ingap
ngs_backbone Roche/Illumina http://bioinf.comav.upv.es/ngs_backbone/index.html
Omixon Variant ABI http://www.omixon.com/omixon/index.html
PyroBayes Roche http://bioinformatics.bc.edu/marthlab/PyroBayes
ssahaSNP Illumina/Roche http://www.sanger.ac.uk/Software/analysis/ssahaSNP
Slider Illumina http://www.bcgsc.ca/platform/bioinfo/software/slider
SNP-o-matic Illumina http://snpomatic.sourceforge.net
SNPSeeker Illumina http://www.genetics.wustl.edu/rmlab/
SNVMix Illumina http://compbio.bccrc.ca
SOAPsnp Roche/Illumina/ABI http://soap.genomics.org.cn
SWA454 Roche http://www.broadinstitute.org/science/programs/genome-biology/crd
SVA Illumina http://www.svaproject.org/
VAAL Illumina http://www.broadinstitute.org/science/programs/genome-biology/crd
VarScan Roche/Illumina http://genome.wustl.edu/tools/cancer-genomics
VARiD Roche/Illumina/ABI http://compbio.cs.utoronto.ca/varid
Differences between genomes
DIAL Illumina http://www.bx.psu.edu/miller_lab/
SomaticCall Illumina http://www.broadinstitute.org/science/programs/genome-biology/crd
SWAP454 Roche http://www.broadinstitute.org/science/programs/genome-biology/crd
VAAL Illumina http://www.broadinstitute.org/science/programs/genome-biology/crd