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CollectHsMetrics Mean_Target_Coverage vs. mean_coverage in PER_TARGET_COVERAGE

Hello,

again a question to picard's CollectHsMetrics. I run it with the parameter PER_TARGET_COVERAGE. I would expect that the mean target coverage reported in the HsMetrics file is the same, as the average of all mean coverages reported in the target coverage file.

But in my cases the value in the metrics file is always higher. Where does this differences come from?

fin swimmer

picard collecthsmetrics
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written by finswimmer finswimmer

1 answer

Argh, it's all about mathematic.

I've forget to include the length of the target regions. Of course the mean coverage over all target regions is sum(mean_target_coverage * length)/sum(length of all target region).

fin swimmer

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written by finswimmer finswimmer

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