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Enhance coverage_stats to report percentage of references with given coverage #22

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peterjc opened this issue Aug 11, 2017 · 0 comments

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@peterjc
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peterjc commented Aug 11, 2017

Example filtering question from discussion with @sj39, What percentage of each reference had at least coverage depth 5?

We could offer a user set single absolute threshold (e.g. min depth 5 reads), a threshold relative to the max or mean (e.g at least half the mean coverage) - and then output an extra column?

Or to avoid complicating the UI, simply compute the fraction of each reference covered at some percentiles of the mean/max coverage? e.g. quartiles relative to the maximum coverage.

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