#!/bin/bash

# variable affectation
vcf_input=$1
out="out_phased"

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