vcf2fasta

converts vcfR format data to Fasta format infile

Usage

vcf2fasta(
  vcf,
  ind_pop,
  keep_pop,
  interleaved = FALSE,
  inc_missing = TRUE,
  out_file = "fasta.fas"
)

Arguments

vcf

-> vcfR object

ind_pop

-> population assignment of individuals in vcf (factor)

keep_pop

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

inc_missing

-> include missing data (logical)

out_file

-> name of file to output (Fasta infile)

Value

nothing

Details

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

Author

Tomas Hrbek August 2022

Examples

vcf2fasta(vcf = my_vcf, ind_pop = ind_pop, keep_pop = keepers, interleaved = FALSE, inc_missing = TRUE, out_file = "Fasta_infile.fas")
#> Error: object 'my_vcf' not found
vcf2fasta(my_vcf, ind_pop, keepers, out_file = "Fasta_infile.fas")
#> Error: object 'my_vcf' not found
vcf2fasta(my_vcf, ind_pop, keepers)
#> Error: object 'my_vcf' not found