vcf2nexus

converts vcfR format data to Nexus format infile

Usage

vcf2nexus(vcf, ind_pop, keep_pop, inc_missing = TRUE, out_file = "nexus.nex")

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

-> population(s) of interest to include in Nexus infile (factor)

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Nexus infile)

Value

nothing

Details

This function converts the vcfR object to a Nexus formatted input file The function will remove indels, and multiallelic loci, and optionally loci with missing data

Author

Tomas Hrbek February 2021

Examples

vcf2nexus(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, inc_missing = TRUE, out_file = "Nexus_infile.nex")
#> Error: object 'my_vcf' not found
vcf2nexus(my_vcf, ind_pop, keepers, out_file = "Nexus_infile.nex")
#> Error: object 'my_vcf' not found
vcf2nexus(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found