Beagle Imputation

Here, I will explain how to impute missing entries in genome-wide marker genotype data. We will use Beagle for the imputation.

Beagle

Download the jar (java archive) file of the latest version of Beagle (Beagle 5.4 on 2023/12/05). You can put the downloaded file anywhere. Here, I assume that you put it in your R working directory.

file.name <- "HDRA-G6-4-RDP1-RDP2-NIAS.AGCT_MAF005MIS001NR"
command <- sprintf(
  "java -Xmx1g -jar beagle.22Jul22.46e.jar gt=%s.vcf.gz out=%s_imputed",
  file.name, file.name)
command
## [1] "java -Xmx1g -jar beagle.22Jul22.46e.jar gt=HDRA-G6-4-RDP1-RDP2-NIAS.AGCT_MAF005MIS001NR.vcf.gz out=HDRA-G6-4-RDP1-RDP2-NIAS.AGCT_MAF005MIS001NR_imputed"
system(command)