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c) Why do I see (......)?
it seems to me that there is a sort of maximum value for the picard collectHsMetrics MEDIAN_TARGET_COVERAGE item, which seems to be 200X. Using various versions of gatk4 (e.g. 188.8.131.52 and 184.108.40.206), on gene panels presenting high coverage (usually mean >= 300X), the MEDIAN_TARGET_COVERAGE is systematically equal to 200.
On larger libraries such as exomes or clinical exomes, when the overall coverage decreases, the result can be 98 or 34 or 125...
Am I completely wrong? If no why is that? (I looked at older analyses made with plain old picard and it was not the case, I had medians > 200X).
And if I am wrong, has anybody experienced this?
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