Question about BAM->CRAM compression and reference sequence files: does the
reference used for CRAM compression/decompression have to be identical to
the one used for aligning the BAM file?
In our pipeline, we periodically create minor revisions of the reference,
e.g. masking a pseudogene region in hg19. We're now considering
re-compressing BAM files aligned with those references to CRAM files (for
long-term storage), but for data durability reasons we'd prefer to use an
hg19 reference from the EBI CRAM reference registry or similar; that way,
we don't have to rely on versioning and long-term storage of all the
reference revisions.
Would this work? I'm less worried about compression efficiency (which I
assume would not be affected as long as the reference revisions are small)
and more about data integrity and durability.
Thanks,
Ziga
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