Hello oncoanalyser team, We have recently switche...
# oncoanalyserh
Harpreet Singh
09/25/2026, 4:23 PMHello oncoanalyser team, We have recently switched to the pipeline version 3.0.0 and wanted to ask if there is a way to publish the alignments as CRAM instead of BAM.
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Stephen Watts
09/25/2026, 11:12 PMHi @Harpreet Singh, the short answer is that the main alignment output can currently only be written as the REDUX BAM
Stephen Watts
09/25/2026, 11:12 PMI have opened a PR for a similar feature as described here that allows users to optionally write 'plain bwa-mem2' CRAM or BAM alignments alongside the REDUX BAM. And this will be included in the 3.1.0 release
Stephen Watts
09/25/2026, 11:14 PMAlso, the 3.0.0 release already accepts CRAM as input, so the remaining piece to complete that story is the above PR (and possibly allowing REDUX to write CRAM eventually, but that is on the Hartwig side)
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Harpreet Singh
09/25/2026, 11:27 PMThanks @Stephen Watts! That clarifies it. Looking forward to the optional bwa-mem2 CRAM/BAM output in 3.1.0. Any rough timeline for when 3.1.0 might land?
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Simon Pearce
10/09/2026, 3:02 PMAlso, the 3.0.0 release already accepts CRAM as input, so the remaining piece to complete that story is the above PR (and possibly allowing REDUX to write CRAM eventually, but that is on the Hartwig side)It amazes me that redux can't write CRAM directly.