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#!/bin/bash
if [ $# -ne 2 ];
then
echo "Usage: $0 [region file] [directory]"
echo
echo "Generates \`basename directory\`.vcf.gz and \`basename directory\`.sites.vcf.gz"
echo "which are the concatenation of files in the directory named [directory]/[region1].vcf.gz,"
echo "[directory]/[region2].vcf.gz, etc. in the order in which they occur in the region file."
echo
echo "Tabix indexes are simultaneously generated."
exit 1
fi
regionfile=$1
mergedir=$2
mergename=$(basename $mergedir)
vcfgenotypes=$mergename.vcf.gz
vcfsites=$mergename.sites.vcf.gz
regions=$(cat $regionfile)
firstfile=$mergedir/$(echo $regions | cut -f 1 -d\ ).vcf.gz
files=$(for region in $regions; do echo $mergedir/$region.vcf.gz; done)
( zcat $firstfile | head -1000 | grep ^#
for file in $files
do
zcat $file | grep -v "^#"
done ) | uniq | pee \
"bgzip >$vcfgenotypes && tabix -p vcf $vcfgenotypes" \
"cut -f -8 | bgzip >$vcfsites && tabix -p vcf $vcfsites"
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