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I have a study including 100 samples. While most samples were sequenced in one lane, a dozen were in two lanes. I wonder if the difference in # of lanes may lead to difference in overall base quality scores after BQSR?
BQSR will process lanes individually if they are correctly identified in the read group information, so it shouldn't cause any difference in the results of BQSR.
Geraldine Van der Auwera, PhD