On 10 Sep 2015, at 21:54, Terry Casstevens <[email protected]> wrote:
> If you use bgzip to zip an already gzipped file, does that result in a
> correctly bgzipped file?
>
> Or should you first ungzip the file and then bgzip?
Your tools are expecting a file with a single layer of bgzipping, so as Peter
noted you will need to undo the existing plain compression and then re-bgzip
it. This can be done without an uncompressed temporary file with
mv foo.vcf.gz foo.vcf.plaingz
gzcat foo.vcf.plaingz | bgzip > foo.vcf.gz
and the final foo.vcf.gz will be identical to what you'd get with "gunzip
foo.vcf.gz; bgzip foo.vcf" [1].
John
[1] Format nerdery: because bgzip doesn't ever put any filenames in the GZIP
header.
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