Can you apply Base Score Recalibration in parallel?

Question

[optimistsso4co3]

Pipeline i analyse uses three steps for recalibration:

1. BaseRecalibrator (in parallel)
2. GatherBQSRReports
3. ApplyBQSR

Is it appropriate to skip 2nd step and applyBQSR on each chunk separately with separate recal.table's ?

[Pierre Lindenbaum]

one you have computed BaseRecalibrator , GatherBQSRReports takes only a few seconds, so there is no use in skipping that part IMHO.

[LChart]

Beyond that, the reports are effectively count tables; and gathering them adds the counts together. If you compute the recalibration table and apply it in the same chunk (say 1MB) then your quality scores will be horribly under-estimated, since the total number of counts will be insufficient for a score of >Q25 or so.