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.

## Details

vars_theta

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

vars_phylo

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

vars_gtrees

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.

vars_ssites

Uses matrices of segregating sites, either in the form of scrm or coala coalescent-simulator object(s), or (2) a ms-style output file.

vars_vcf

Uses a variant call format (VCF) file that directly specifies variants. This method does not work if the vcfR package isn't installed.

create_variants