SNVMix 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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Maintainers


  • person_outline Sohrab Shah <>
  • person_outline Rodrigo Goya <>

Publication for SNVMix

SNVMix IN pipeline

2013
PMCID: 3823931
PMID: 24244370
DOI: 10.1371/journal.pone.0078823

[…] at the 5% level but corrected for multiple testing using the bonferonni correction., allele counts for heterozygous variants were attained for both the genome and the transcriptome using snvmix2 [16] (once complete genomics data had been converted using the cg2bam tools provided in the cgatools package). allelic imbalance was tested only in those genes deemed as expressed […]

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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