SNVMix

SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes:  aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).  A tool for fitting the model using expectation maximization is also supplied (use -T option).

 

Documentation

  • SNVMix web site
  • Sohrab P. Shah, Ryan D. Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Giuliany, Janine Senz, Christian Steidl, Robert A. Holt, Steven Jones, Mark Sun, Gillian Leung, Richard Moore, Tesa Severson, Greg A. Taylor, Andrew E. Teschendorff, Kane Tse, Gulisa Turashvili, Richard Varhol, Rene L. Warren, Peter Watson, Yongjun Zhao, Carlos Caldas, David Huntsman, Martin Hirst, Marco A. Marra and Samuel Aparicio.Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. vol461, 809-813. (2009)
  • Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics . 2010 Mar 15;26(6):730-6. 

 

Usage

  • Bridges

To see what versions of SNVMix are available type

module avail snvmix

To see what other modules are needed, what commands are available and how to get additional help type

module help  snvmix

To use SNVMix, include a command like this in your batch script to load the SNVMix module:

module load snvmix

Be sure you also load any other modules needed, as listed by the module help snvmix command.

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