1#!/bin/bash 2 3if [ $# -ne 2 ]; 4then 5 echo "Usage: $0 [region file] [directory]" 6 echo 7 echo "Generates \`basename directory\`.vcf.gz, which is the concatenation" 8 echo "of files in the directory named [directory]/[region1].vcf.gz," 9 echo "[directory]/[region2].vcf.gz, etc. in the order in which they" 10 echo "occur in the region file." 11 echo 12 echo "A tabix index is subsequently generated." 13 exit 1 14fi 15 16regionfile=$1 17mergedir=$2 18mergename=$(basename $mergedir) 19vcfgenotypes=$mergename.vcf.gz 20#vcfsites=$mergename.sites.vcf.gz 21 22firstfile=$mergedir/$(head -1 $regionfile).vcf.gz 23files=$(for region in $(cat $regionfile); do echo $mergedir/$region.vcf.gz; done) 24 25zcat $firstfile | head -1000 | grep ^# 26for file in $files 27do 28 zcat $file | grep -v "^#" 29done 30