SNVMix
Application data |
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Biological application domain(s) | SNP discovery |
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Maintained? | Maybe |
Input format(s) | Maq, SAM |
Programming language(s) | C |
Licence | open-source |
Summary: 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).
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