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