#!/bin/bash

# variables affectation
vcf_input=$1
ref=$2
out="out_imputed"

# create temporary directory
directory=`dirname $0`
mkdir tmpdir$$
cp -rf $vcf_input tmpdir$$/input.vcf
# launch beagle
java -Xmx2g -jar $directory/beagle.jar ref=$ref gt=$vcf_input out=$out
# remove temporary dir
rm -rf tmpdir$$