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Recalibration with non-model organism
I regularly use GATK for non-model organism analysis, and have been thinking a bit about recalibration (so far I have not tried this).
There seem to be two steps in the workflow that benefit - base quality score recalibration, and variant quality recalibration. There also appear to be two methods of generating 'true' variant sets for non-model organisms : (1) an iterative approach, where you run through GATK and take the initial variant set (based on hard filters) and use this for recalibration; and (2) one could manually curate a small section of the genome for high quality variants.
I expect approach (1) would have good sensitivity, while approach two would have good specificity. What is more important (sensitivity or specificity) for the recalibration? Is this the same for both types of recalibration?
Thanks in advance for your insights,