Can you apply Base Score Recalibration in parallel?
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12 months ago

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 ?

wgs • 535 views
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one you have computed BaseRecalibrator , GatherBQSRReports takes only a few seconds, so there is no use in skipping that part IMHO.

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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.

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