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.
run.beagle5(
beaglejar,
vcfpath,
reffile,
outpath,
plinkfile,
nthreads = 1,
window = 40,
overlap = 4,
maxheap.gb = 10,
javajre = "java"
)character string path to Beagle5 java jar file
character string path to the vcf input file to be phased
character string path to the Beagle5 reference file
character string path to Beagle's output vcf.gz file
character string path to the plink file
integer number of threads
integer max size of genomic window to be phased (cM; default 40; decrease for less memory usage; should be >1.1*overlap)
integer overlap of windows (cM; default 4)
integer maximum heap size for the java process in gigabytes (default 10)
Path to the Java JRE executable (default java, i.e. in $PATH)