run.beagle5: Command to run beagle5
In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

run.beagle5

R Documentation

Command to run beagle5

Description

This runs beagle through a system call to the beagle java jar file. It requires pre-formatted reference and plink files for the correct genome build.

Usage

run.beagle5(
  beaglejar,
  vcfpath,
  reffile,
  outpath,
  plinkfile,
  nthreads = 1,
  window = 40,
  overlap = 4,
  maxheap.gb = 10,
  javajre = "java"
)

Arguments

`beaglejar`	character string path to Beagle5 java jar file
`vcfpath`	character string path to the vcf input file to be phased
`reffile`	character string path to the Beagle5 reference file
`outpath`	character string path to Beagle's output vcf.gz file
`plinkfile`	character string path to the plink file
`nthreads`	integer number of threads
`window`	integer max size of genomic window to be phased (cM; default 40; decrease for less memory usage; should be >1.1*overlap)
`overlap`	integer overlap of windows (cM; default 4)
`maxheap.gb`	integer maximum heap size for the java process in gigabytes (default 10)
`javajre`	Path to the Java JRE executable (default java, i.e. in $PATH)