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tools using CRAM format?

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

cram
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updated by Ram Ram • written by Richard Richard

1 answer

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 (?)

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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