Dear GATK Team,
In the tutorial (How to) Map and clean up short read sequence data efficiently, it states that MergeBamAlignment (Picard) 'restores original base quality scores'. My understanding is that this would include changing the base quality scores set at 2 for clipped regions (e.g. adapter sequences) marked with the XT tag back to original scores. Does this mean clipping status is lost and therefore, adapter sequences will be considered in downstream analyses?
If this is the case, BQSR, HaplotypeCaller, Mutect2 and other downstream tools could potentially consider problematic sequences (e.g. adapter sequences) in contrast to what has been described in previous posts. Therefore, clarification would be appreciated.
Thank you for your time and help.
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