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#!/bin/bash
if [ $# -ne 2 ];
then
echo "Usage: $0 [region file] [directory]"
echo
echo "Generates \`basename directory\`.vcf.gz, which is the concatenation"
echo "of files in the directory named [directory]/[region1].vcf.gz,"
echo "[directory]/[region2].vcf.gz, etc. in the order in which they"
echo "occur in the region file."
echo
echo "A tabix index is subsequently generated."
exit 1
fi
regionfile=$1
mergedir=$2
mergename=$(basename $mergedir)
vcfgenotypes=$mergename.vcf.gz
#vcfsites=$mergename.sites.vcf.gz
firstfile=$mergedir/$(head -1 $regionfile).vcf
files=$(for region in $(cat $regionfile); do echo $mergedir/$region.vcf; done)
( cat $firstfile | head -1000 | grep ^#
for file in $files
do
cat $file | grep -v "^#"
done ) | ( bgzip >$vcfgenotypes && tabix -p vcf $vcfgenotypes )
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