vars_functions: Organize higher-level information for creating variants.

Description Details See Also


The following functions organize information that gets passed to create_variants to generate variants from a reference genome. Each function represents a method of generation and starts with "vars_". The first three are phylogenomic methods, and all functions but vars_vcf will use molecular evolution information when passed to create_variants.



Uses an estimate for theta, the population-scaled mutation rate, and a desired number of variants.


Uses phylogenetic tree(s) from phylo object(s) or NEWICK file(s), one tree per chromosome or one for all chromosomes.


Uses gene trees, either in the form of an object from the scrm or coala package or a file containing output in the style of the ms program.


Uses matrices of segregating sites, either in the form of scrm or coala coalescent-simulator object(s), or a ms-style output file.


Uses a variant call format (VCF) file that directly specifies variants.

See Also


jackalope documentation built on Dec. 1, 2019, 1:17 a.m.