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CRAM output #294

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dbrami opened this issue Mar 5, 2022 · 1 comment
Open

CRAM output #294

dbrami opened this issue Mar 5, 2022 · 1 comment
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enhancement Improvement for existing functionality

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@dbrami
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dbrami commented Mar 5, 2022

Description of feature

How can I add a step to compress BAM to CRAM once the analysis is complete, then delete BAMs?
The alternative would be to output CRAM in lieu of BAM but not sure all the downstream processes can ingest CRAM.
@dbrami dbrami added the enhancement Improvement for existing functionality label Mar 5, 2022
@drpatelh
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drpatelh commented Mar 7, 2022

Hi @dbrami ! Hope you are well!

Yes, I think we should definintely look into adding this feature in the next release. Not entirely sure where and if we can hack the pipeline to produce it in the current release. Would need to sit down and have a play but suggestions welcome.

not sure all the downstream processes can ingest CRAM.

Agreed and this would definitely be the better option. Given the number of tools used in say the Illumina processing arm of the pipeline this would take some compatibility testing and implementation too.

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@dbrami @drpatelh