The Turnkey Variant Analysis Project

The Turnkey Variant Analysis Project (TVAP) focuses on the discovery and interpretation of genetic variants by providing a computational framework and high throughput data analysis tools for use with the latest DNA sequencing technologies. TVAP is flexible and powerful enough to be adopted by experienced laboratories, while at the same time providing high quality, push-button analysis of sequence data for those with little bioinformatics expertise. More.

TVAP will enable widespread and easy analysis and interpretation of genetic data, accelerating the overall understanding of genetic information and its application to human health. Click on a tool for more information, download, installation and support links.

Detection Tools

Bassovac
Improved Bayesian inversion somatic caller

BreakDancer
SV caller using paired-end sequence data

CMDS
Recurrent CNV caller using population data

CopyCat
A read depth based copy number caller

GenomeVIP
Genome Variant Investigation Platform

MSIsensor
Microsatellite instability detection using paired tumor-normal

PASSion
Paired-end RNA-Seq splice site detection

Pindel
Indel caller using pattern growth

SomaticSniper
Bayesian somatic SNV caller

SquareDancer
Split reads for SV discovery

TIGRA_SV
De novo assembly of SV breakpoints

VarScan
Germline and somatic SNV and CNV caller

Infrastructure Tools

GMS
Genome Modeling System

Interpretation Tools

HotSpot3D
3D hotspot mutation proximity analysis tool

MuSiC
A suite of variant interpretation tools

PathScan
Pathway analysis tool using population data

SciClone
Infer subclonal architecture of tumors

Visualization Tools

Lolliplot
A mutation distribution graphics tool

Pairoscope
SV visualization tool