bgzip all VCF files in a directory?

So I’ve been trying to bgzip around 100 VCF files in parallel, but although the jobs are submitted and files get created there’s definitely something wrong.

So far I’ve been trying:

$for file in *.vcf 

> do

> bsub /foo/bar/bgzip $file

>> $file.gz 

What is the correct way to do this?

Thanks in advance!

Answer

If, as my websearches suggest, bgzip works the same way as gzip, you don’t specify an output file:

for f in *.vcf; do
   bsub bgzip "$f"
done

You should also double-quote variables in case your filenames have spaces in them.