Takes vcf file and writes to vcf.gz OR takes gz filename as arguments and reads from stdin.

bgziptabix.sh

#!/bin/bash

f=$1
extension=${f##*.}

if [[ "$extension" == 'vcf' ]]
then
    in=$f
    out=${in}.gz
    bgzip $in > $out
    tabix -f -p vcf $out
elif [[ "$extension" == 'gz' ]]
then
    out=$f
    #read from standard input
    bgzip > $out
    tabix -f -p vcf $out
fi