SNVMix statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SNVMix
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Tool usage distribution map

This map represents all the scientific publications referring to SNVMix per scientific context
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Protocols

SNVMix specifications

Information


Unique identifier OMICS_00077
Name SNVMix
Alternative name SNVMix2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, Perl
License MIT License
Computer skills Advanced
Version https://github.com/shahcompbio/snvmix/archive/master.zip
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline Sohrab Shah
  • person_outline Rodrigo Goya

Publication for SNVMix

SNVMix citations

 (18)
library_books

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

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] 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 JointSNVMix2 and Virmid, infers the posterior probability of […]

library_books

Comprehensive benchmarking of SNV callers for highly admixed tumor data

2017
PLoS One
PMCID: 5636151
PMID: 29020110
DOI: 10.1371/journal.pone.0186175

[…] also saw high variability among callers and declining sensitivity with increasing admixture levels for all tools (). Precision was very high for all tools and admixture levels, except for SNVSniffer, SNVMix2, SAMtools and FreeBayers for admixture levels above 60%. […]

library_books

Molecular etiology of an indolent lymphoproliferative disorder determined by whole genome sequencing

2016
PMCID: 4849852
PMID: 27148583
DOI: 10.1101/mcs.a000679

[…] scriptome shotgun sequencing) pipeline coverage analysis (v1.1) using the “stranded” option to determine gene and exon read counts and normalized expression level. Expressed variants were called with SNVMix2 (v0.12.1-rc1) () and SAMtools (v0.1.17). Gene expression in the tumor was compared with a compendium of normal tissues and to one or more normal libraries from the same tissue type to identify […]

library_books

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy

2015
PLoS One
PMCID: 4687867
PMID: 26695660
DOI: 10.1371/journal.pone.0145176

[…] (http://www.novocraft.com/). Realignment and recalibration were performed using GATK [](VN: 2.7-4-g6f46d11) Best Practices version 3. Germline variations were called with GATK’s UnifiedGenotyper and SNVMix2[]. Variant quality score was recalibrated using the following command-line optimizations: for SNVs, -an QD -an MQRankSum -an ReadPosRankSum -an FS -an DP; and for INDELs, -an DP -an FS -an Rea […]

library_books

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

2015
Biomed Res Int
PMCID: 4619817
PMID: 26539496
DOI: 10.1155/2015/456479

[…] e genome sequencing.Lastly, we considered a large number of aligners [–] and variant callers [–] but ultimately chose the 11 tools based on prevalence, popularity, and relevancy to our dataset (e.g., SNVMix, VarScan2, and MuTect were not used as they are intended for use on tumor-derived samples). Our analysis itself involves comparing six aligners (Bowtie2 [], BWA sampe [], BWA mem [], CUSHAW3 [] […]

library_books

Whole Genome Analyses of a Well Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements

2014
PLoS One
PMCID: 3914808
PMID: 24505276
DOI: 10.1371/journal.pone.0087113

[…] er (BWA). Post-alignment processing included local realignment with Genome Analysis Toolkit (GATK) .Single nucleotide variants (SNV) and insertions/deletions (indel) were detected utilizing GATK and SNVMix . Identified variants were then placed in the custom annotation pipeline and SNV and indel reports created. SNVMix filtered (probability ≥0.8) variant calls from TREAT were used to extract tumo […]


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SNVMix institution(s)
Department of Molecular Oncology Breast Cancer Research Program, British Columbia Cancer Research Centre, Vancouver, BC, Canada; Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Centre for Translational and Applied Genomics of British Columbia Cancer Agency, Vancouver, BC, Canada; Provincial Health Services Authority Laboratories, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
SNVMix funding source(s)
Supported by the Canadian Institutes for Health Research (CIHR), and the Michael Smith Foundation for Health Research (MSFHR) and the Canadian Breast Cancer Foundation.

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