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BaseRecalibrator on tiny gene panel with deep coverage?
I am currently working on data from a tiny gene panel (~29 kb; target enrichment by amplicons) with deep coverage in most of the samples (mean coverage well above 1000x in most samples).
I have read the basics of
BaseRecalibrator here and according to the rule of thumb quoted below, I should not apply
BaseRecalibrator to this dataset:
This procedure will not work well on a small number of aligned reads. We usually expect to see more than 100M bases per read group; as a rule of thumb, larger numbers will work better
However, in the next paragraph it is stated:
No excuses You should almost always perform recalibration on your sequencing data.
Hence, what is the best choice here? Is this one of those "almost always" exceptions to the rule of thumb?