Hi, for an assay developed by my vendor, I ran latest Picard HsMetrics (2.21.8) with two different options for the same set of BAM files: one with a NEAR_DISTANCE=250 and one with NEAR_DISTANCE=0. The bait and Target interval file was the same. With the default value of NEAR_DISTANCE=250, I got ON_BAIT_VS_SELECTED value around 0.45 for my 12 samples and with NEAR_DISTANCE=0 I got it around 0.5.
ON_BAIT_VS_SELECTED is defined as the fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES). In the 2nd case, since my near_distance = 0 it means that all the bases are either on the bait or outside the near distance so near_bait_bases = 0 which means that I should see ON_BAIT_VS_SELECTED = 1 but I see it around 0.5. Am I misunderstanding anything?
The other question I have is: if both my Target and Bait files are the same, why is my mean target coverage around 2000X where as mean bait coverage is 3000X.
Thank you for your help in advance!