SNVMix

Application data
Biological application domain(s)	SNP detection
Maintained?	Maybe
Input format(s)	Pileup
Programming language(s)	C
Licence	MIT

Summary: Detects single nucleotide variants from next generation sequencing data.

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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).

Links

• SNVMix Source code [ edit link ]

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References

1. . 2010. Bioinformatics

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