SiNVICT specifications


Unique identifier OMICS_12625
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.0
Stability Stable
g++, Boost
Maintained Yes




No version available



  • person_outline S. Cenk Sahilp

Publication for SiNVICT

SiNVICT citations


A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] nput (). In addition, several algorithms are dedicated to perform single-sample variant calling. These algorithms include SNVMix2, shearwater, SPLINTER, SNVer, OutLyzer, Pisces, ISOWN, SomVarIUS, and SiNVICT , , , , , , , , and fall into two categories.SNVMix2, Shearwater, SPLINTER, SNVer, OutLyzer, and Pisces report all variants without distinguishing somatic and germline. SNVMix2’s, like JointS […]


Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

BMC Bioinformatics
PMCID: 5209852
PMID: 28049408
DOI: 10.1186/s12859-016-1417-7

[…] We compared the nine somatic variant calling programs deepSNV [], Genome Analysis Toolkit (GATK) HaplotypeCaller (HP) [–], GATK UnifiedGenotyper (UG) [–], JointSNVMix2 [], MuTect [], SAMtools [], SiNVICT [], SomaticSniper [], and VarScan2 []. Figure illustrates the workflow for the comparison in a flowchart. A heterogeneous cancer sample was simulated based on a real renal cell carcinoma samp […]

SiNVICT institution(s)
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; MADD-Gen Graduate Program, Simon Fraser University, Burnaby, BC, Canada; School of Informatics and Computing, Indiana University, Bloomington, IN, USA; Vancouver Prostate Centre, Vancouver, BC, Canada; Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; School of Informatics and Computing, Indiana University, Bloomington, IN, USA
SiNVICT funding source(s)
Supported by NSERC Create MADD-Gen Training programme, NSERC Discovery Frontiers grant on ‘Cancer Genome Collaboratory’, Genome Canada and Canadian Cancer Society Research Institute Innovation grants, Terry Fox Research Institute New Frontiers Program (grant no. TFF116129), Canadian Cancer Society (grant no. 702837) and Prostate Cancer Canada (grant no. D2014-13) and in part by the Movember Foundation.

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