Difference between bait and target region

[Brambo]

Hi all,

I am using CalculateHsMetrics.jar of PicardTools.
Although I defined my targetinterval exactly the same as my bait interval (BAIT_INTERVALS=$targetInterval TARGET_INTERVALS=$targetInterval), my mean_bait_coverage and mean_target_coverage in my output file do differ ( 600X vs 2X) What can be the reason for this?

thanks in advance,

[david_2012]

Wondered the same thing and found your post DuckDuckGoing it. Eventually figured out the little difference in how they are computed, according to the documentation (http://broadinstitute.github.io/pica...ml#HsMetrics):
MEAN_BAIT_COVERAGE The mean coverage of all baits in the experiment.
MEAN_TARGET_COVERAGE The mean coverage of targets that received at least coverage depth = 2 at one base.

I think the difference is that the mean target coverage is only calculated for targets where at least one base has a coverage of 2 or higher. However, mean bait coverage is calculated for ALL baits, including those with no coverage at all. You would thus expect these (almost) no coverage baits to drag down the average to a lower value, which is what I see.