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grbot / varcall

Nextflow scripts for doing variant calling on human samples
MIT License
8 stars 13 forks source link

combine-lanes improvement #45

Closed melnel000 closed 1 year ago

melnel000 commented 2 years ago

Hi Gerrit

It would be great if you could modify the combine-lanes workflow to write a CRAM file as output with the extension .md.recal.cram so that it is consistent with the rest of the pipeline. Just a suggestion as at the moment we have to run bam-to-cram after combine-lanes and also rename the cram files with .md.recal.cram.

Thanks, Melissa

grbot commented 1 year ago

@melnel000 did we fix this at the end?

melnel000 commented 1 year ago

No it was not fixed. Workflow works though, it was just a suggested improvement to make things simpler.

grbot commented 1 year ago

Ok now see the isssue. I do not want to assume the combined files have already been marked with duplicates and recalibrated. If you can manage with your process for now it will be great. I will think if there is a better sollution.