--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/execute_beagle.sh	Tue Aug 14 07:59:19 2018 -0400
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+
+vcf_input=$1
+phase=$2
+impute=$3
+out_prefix="out"
+
+mkdir tmpdir$$
+
+cp -rf $vcf_input tmpdir$$/input.vcf
+
+beagle gt=$vcf_input phase-its=$phase impute-its=$impute out=$out_prefix
+
+gunzip $out_prefix.vcf.gz
+
+rm -rf tmpdir$$
+