Re: [Samtools-help] CRAM index files

[jkb <jk...@sa...>]

 

On 2015-08-12 17:20, David Roazen wrote: 

> htsjdk (https://github.com/samtools/htsjdk/ [1]), 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.

Or a need for GATK to start supporting CRAI. 

I'm not yet convinced that abusing BAI to index something with a non-32k
(or is it 64k?) block size format is the best way to go. Admittedly
though I haven't investigated how it works as initially I just assumed
it would be impossible. CRAM isn't a bgzf stream so I didn't explore
further. I think it does something like treat containers as reads
instead, but I'm not sure on practically what that means for index
efficiency. 
 

Links:
------
[1] https://github.com/samtools/htsjdk/



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