C>T SNPs about methyldackel HOT 4 CLOSED

Thanks for the question! At the moment this issue is simply ignored, due to this package having been developed in the context of in bred mice, where variants are simply not an issue. It'd be a simple enough thing to implement though, so I'll leave this here as a reminder to do so (I've actually been thinking of doing it for almost 1.5 years, but never had someone outside of my group ask me about it).

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I've implemented a method to do this in the master branch, it'll be part of the next release. The method is fairly simple, though I know it's also used in at least some other tools. Namely, it looks for mismatches in the strand opposite of a C and will exclude a site (or CpG/CHG if --mergeContext is specified) if the fraction of mismatches is above some desired value (--maxVariantFrac). For obvious reasons, there's also a minimum depth required for this (--minOppositeDepth).

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Thank you! I will give this a try

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This is now implemented in version 0.3.0 :)

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