vcfregionreduce_and_cut

#!/bin/bash
# Reduce, gzip, and tabix

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"