tools using CRAM format?

Question

[Richard]

Hi all,

I've been asked to take a look at CRAM format for out pipeline.

Are there any users who can tell me if they use it in a somatic pipeline? I'd like to be able to identify somatic CNVs, Structural breakpoints, and SNVs, and I'm wondering if people would usually just store their files are CRAM and convert to BAM for analysis, or if there are available workflows that use CRAM natively.

Alternately, maybe people are just use CRAM for archiving data once analysis is complete?

I'm a newbie, so any information would be helpful.

Thanks,
Richard

Answer 1

[Pierre Lindenbaum]

samtools already uses CRAM

The java htsjdk team is currently building a CRAM Api: https://github.com/samtools/htsjdk/search?utf8=%E2%9C%93&q=CRAM

GATK uses htsjdk and should soon use this format (?)

@yokofakun Incomplete. #GATK dev nightlies have basic support for reading and writing CRAM but no indexing, so no interval seeking yet.

— GATK Dev Team (@gatk_dev) March 10, 2015