We want the DoC calculations for CNVs to include N bases in the reference just so that the PAR regions in chr Y (set to all Ns) end up with mean coverage of 0/L, where L = target length (and not NaN = 0/0). Including Ns in any other targets is probably OK too, since most (if not all) non-chromosome Y targets will not have any Ns

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Menachem Fromer 2012-03-28 16:42:34 -04:00

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