get.vcf: Generate vcf-file

In MoBPS: Modular Breeding Program Simulator

Generate vcf-file

Description

Generate a vcf-file for selected groups and chromosome

Usage

get.vcf(
  population,
  path = NULL,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  id = NULL,
  chromosome = "all",
  non.genotyped.as.missing = FALSE,
  use.id = FALSE,
  file.append = FALSE
)

Arguments

population	Population list
path	Location to save vcf-file
database	Groups of individuals to consider for the export
gen	Quick-insert for database (vector of all generations to export)
cohorts	Quick-insert for database (vector of names of cohorts to export)
id	Individual IDs to search/collect in the database
chromosome	Limit the genotype output to a selected chromosome (default: "all")
non.genotyped.as.missing	Set to TRUE to replaced non-genotyped entries with "./."
use.id	Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names
file.append	Set extend an existing vcf-file ((without writting a header))

Value

VCF-file for in gen/database/cohorts selected individuals

Examples

data(ex_pop)

file_path <- tempdir()
get.vcf(path=file_path, ex_pop, gen=2)
file.remove(paste0(file_path, ".vcf"))

MoBPS documentation built on Nov. 5, 2025, 6:26 p.m.