Dear GATK Team,
In the tutorial (How to) Map and clean up short read sequence data efficiently, the documentation states that changing the base quality scores to 2 for a clipped region 'effectively removes the adapter portion of sequences from contributing to downstream read alignment and alignment scoring metrics'. However, from my understanding, BWA-MEM does not take into account base quality scores. Therefore, how does this work?
Thank you for your time and help.
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