SNVMix2
:: DESCRIPTION
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).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/MacOsX
- Samtools
:: DOWNLOAD
:: MORE INFORMATION
Citation
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.