annotate beagle_impute.sh @ 21:1efd84f03444 draft

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#!/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$$