--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beagle_impute.sh	Fri Oct 21 06:30:52 2016 -0400
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+
+vcf_input=$1
+ref=$2
+out="out_imputed"
+
+directory=`dirname $0`
+
+mkdir tmpdir$$
+
+cp -rf $vcf_input tmpdir$$/input.vcf
+
+
+java -Xmx2g -jar $directory/beagle.jar ref=$ref gt=$vcf_input out=$out
+
+
+rm -rf tmpdir$$
\ No newline at end of file