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changeset 18:27fb6c2a98a3 draft

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Uploaded
author nicolas
date Fri, 21 Oct 2016 06:30:52 -0400
parents 58b58d95b0e0
children 4e97cb4310ac
files beagle_impute.sh
diffstat 1 files changed, 18 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /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$$
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