OctopusPolyclone
The polyclone calling model is designed for calling variation in a pooled sample of haploid genomes where the number and mixture composition of genomes is unknown. The model will attempt to deconvolute haplotypes and call the number of local haplotypes, in addition to variants on called haplotypes. Use cases include bacterial or viral metagenomics, mixed infection analysis, and mitochondria sequencing.
Usage#
The polyclone calling model is invoked by speciying the polyclone --caller.
VCF output#
Performance considerations#
The most important parameter in this model is --max-clones which determines the maximum number of haplotypes that octopus will try to use to fit the data. This is a bit like setting the 'ploidy' for the sample. Higher values of --max-clones may lead to longer runtimes and more memory usage - we do not recommend values above 10.