htsjdk (https://github.com/samtools/htsjdk/), and software built on top of it such as the GATK, currently only support BAI indices with CRAM files. It also appears likely that when CRAI support is added to htsjdk, it will be implemented internally as an on-the-fly CRAI -> BAI conversion.
So, there is a bit of a need right now for samtools index -b <cram_file> to honor the "-b" option and create a BAI index on a CRAM file. David On Wed, Aug 12, 2015 at 12:03 PM, jkb <[email protected]> wrote: > On 2015-08-07 16:50, Edward Kwiatkowski wrote: > > I want to create a BAI on a CRAM. When I do > > samtools index -b xyz.cram > > > it still gives me a CRAI instead. How can I use samtools to produce BAI's > from CRAM files? > > Samtools doesn't support use of BAI for CRAM. We use BAI for BAM and CRAI > for CRAM only. Can you elaborate why you require BAI for CRAM please? > > Thanks, > > James > > > -- 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 > >
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