I'm currently using Picard v2.27.4 and I'm calculating HSMetrics over several BAM files. What is not clear for me is how MEAN_TARGET_COVERAGE and MEAN_BAIT_COVERAGE are calculated. For what I know by now, these 2 parameters are obtained by these formulas:
MEAN_TARGET_COVERAGE = ON_TARGET_BASES/TARGET_TERRITORY
MEAN_BAIT_COVERAGE = ON_BAIT_BASES/BAIT_TERRITORY
(In my case TARGET_TERRITORY = BAIT_TERRITORY)
According to the PTC_EXC fields (and subtracting from PF_BASES_ALIGNED the respective excluded bases), it is still not clear how ON_TARGET_BASES and ON_BAIT_BASES are obtained. Can you give me an insight about this part?
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