Compress already compressed file with bgzip without decompressing first

Question

[miles.anderson]

I have a large compressed VCF that needs to be compressed with bgzip so I can run bcftools. However, it isn't compressed with bgzip and if I decompress I will go over my quota on the cluster. Is it possible to compress a file without decompressing it fully and then compressing it again?

Answer 1

[4galaxy77]

Assuming it's compressed with gzip, then zcat it to stdout which won't use up any of your disk quota and then bgzip.

zcat vcf.gz | bgzip -c > vcf.bgz