Infrastructure

GenomeVIP 
Cloud based Genome Variant Investigation Platform [github]

Variant DETECTION 

Bassovac 
Improved Bayesian inversion somatic caller [presentation] [github]

BreakDancer
SV caller using paired-end sequence data [video] [publication] [github]

CMDS
Recurrent CNV caller using population data [publication] [github]

MSIsensor 
Microsatellite instability detection using paired tumor-normal [publication] [github]

PASSion 
Paired-end RNA-Seq splice site detection [publication] [github]

Pindel-c
Indel caller using pattern growth [publication[publication] [github]

SomaticSniper
Bayesian somatic SNV caller [video] [publication] [github]

SquareDancer 
Split reads for SV discovery [video] [github]

TIGRA_SV 
De novo assembly of SV breakpoints [publication] [download]

VarScan
Germline and somatic SNV and CNV caller [publication] [github]

VirusScan
Detect virus from next generation sequencing data [publication] [github]

Interpretation

HotSpot3D 
3D hotspot mutation proximity analysis tool [publication] [github]

MuSiC
A suite of variant interpretation tools [publication] [github]

PathScan 
Pathway analysis tool using population data [publication]

SciClone
Infer subclonal architecture of tumors [publication] [github]

Visualization

Breakpoint Surveyor 
A comprehensive pipeline to analyze and visualize structural variants [github]

Lolliplot
A mutation distribution graphics tool

Pairoscope
SV visualization tool [github]