MoBPS (version 1.13.1)

get.vcf: 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
)

Value

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

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))

Examples

data(ex_pop)
# \donttest{
file_path <- tempdir()
get.vcf(path=file_path, ex_pop, gen=2)
file.remove(paste0(file_path, ".vcf"))
# }