Can Sarek use mixed input formats, e.g. FASTQ and BAM files, in the same samplesheet?

yes

Hmm, guess it doesn't save me anything then. No worries, was just wondering.

yeah the

step

is the limiting factor here

We have been thinking about allowing for mixing multiple steps in the same samplesheet, but too much of a headache for now

For context, we have models (cell line/xenos) with patient germline data. The xenos need to be mapped separately, as they have contaminating mouse reads - was hoping to just re-use the aligned germline bams.

makes sense. I am afraid right now it'll need to be to samplesheets 😕

I would bring all samples to the state where you have mapped/deduplicated/BQSR CRAMs/BAMs and then use those in a separate run starting with

--step variant_calling

.

I'm guessing we could get there by skipping all preprocessing tools