pedmap.to.phasedbeaglevcf: Internal function to perform imputing/phasing

In MoBPS: Modular Breeding Program Simulator

Description

Internal function to perform imputing/phasing (path chosen for the web-based application)

Usage

pedmap.to.phasedbeaglevcf(
  ped_path = NULL,
  map_path = NULL,
  vcf_path = NULL,
  beagle_jar = "/home/nha/beagle.03Jul18.40b.jar",
  plink_dir = "/home/nha/Plink/plink",
  db_dir = "/home/nha/Plink/DB/",
  verbose = TRUE
)

Arguments

ped_path	Directory of the ped-file
map_path	Directory of the map-file
vcf_path	Directory of the vcf-file (this will override any ped/map-file input)
beagle_jar	Directory of BEAGLE
plink_dir	Directory of Plink
db_dir	Directory to save newly generated files (ped/map will be stored in the original folder)
verbose	Set to FALSE to not display any prints

Value

Phased vcf file in vcf_path

MoBPS documentation built on Nov. 9, 2021, 5:08 p.m.