Does anyone have insight into what happens if you apply BQSR twice to a sample?
The case here is that we might run a pipeline that aligns and runs BQSR, then we throw away the original fastqs. If we later want to realign, we can regenerate fastqs, but the original quality scores are gone. What would the effect be of running them through a pipeline that applies BQSR a second time?
Obviously we could modify the pipeline to omit BQSR on a subsequent run, but I wonder if that's even necessary. Anyone with more insight into the underlying algorithm know what the effect would be? In general terms, is it going to be worse, or largely inconsequential?