pedmap.to.phasedbeaglevcf {MoBPS}

Internal function to perform imputing/phasing

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