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Compress already compressed file with bgzip without decompressing first

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?

bgzip
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updated by 4galaxy77 4galaxy77 • written by miles.anderson • miles.anderson

1 answer

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
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written by 4galaxy77 4galaxy77

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