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Ignore duplicates and failed QC reads in CoverageDepth? #29

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tavinathanson opened this issue Apr 5, 2017 · 0 comments

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tavinathanson commented Apr 5, 2017

From @tavinathanson:

@ryan-williams i wonder if one of the differences between pageant coverage depth output and other coverage tools lies in the handling of marked dups? (thinking back to some of the discrepancies we've seen in the past, not clear if they were all addressed) -- do you know if e.g. bedtools coverage ignores marked dups?
relevant https://www.biostars.org/p/195497/#195543

From @ryan-williams:

cool, yea i can add dupe/qcfail filtering if you like

From @tavinathanson:

seems like it'd be good for coveragedepth defaults to be similar to other tools in the space, what do you think?

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