Thank you Peter and John!
On Fri, Sep 11, 2015 at 5:30 AM, John Marshall <[email protected]> wrote: > 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. > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
