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nf-core / exoseq

Please consider using/contributing to https://github.com/nf-core/sarek
http://nf-co.re
MIT License
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Make CRAM default alignment format #14

Closed marchoeppner closed 5 years ago

marchoeppner commented 6 years ago

Include the --bam switch and make CRAM the default output for BWA and ApplyBQSR

maxulysse commented 6 years ago

I'm all for the new stuff, but as CRAM is the newest format, shouldn't BAM be the default output format and CRAM the optional? Aren't we loosing some quality information at some point with enforcing CRAM?

marchoeppner commented 6 years ago

Lossless CRAM should be fine; I am more thinking of the "educational" aspect. We are really trying to push CRAM since the information content is equivalent, but storage requirements reduced by about 40%. For sequencing centers in particular (but any bfx user, really), this is quite significant. If you make CRAM the optional format, noone will use it