aligned or unaligned bam files?

[nnneeennn]

Ask away!

Hi,

in your quickstart you mention that this pipeline works only with aligned bams, however the nextflow_schema.json asks for aligned or unaligned bam files for both tumor and normal bams. This is also the info you get when running nextflow run epi2me-labs/wf-somatic-variation --help.

I have previously started this workflow from unaligned bam files and did not get an error, now I am wondering whether I need to rerun from aligned bams instead?

Thank you, Nina

[TBradley27]

Just to add to this, I was able to also run the pipeline from unaligned bams, which seemed to run successfully

The reason I used unaligned bams, is that, at this point I am not sure how to use an aligner such as minimap2 and to preserve base modification information

[RenzoTale88]

Hi @nnneeennn, @TBradley27 yes, the workflow accepts both aligned and unaligned BAM (uBAM) files. Providing an unaligned/aligned to a different reference BAM will cause the workflow will automatically perform a mapping of the sequences prior to downstream analyses.

@TBradley27 just to reassure you, when working with an uBAM file the workflow will preserve the details of the modified bases in the MM/ML fields used for the downstream tools. You can see how we remap the sequences with minimap2 here.

I hope this helps. Andrea

[nnneeennn]

should your readme be updated to reflect this?

[RenzoTale88]

There will be an extensive update of the README in the next release.