The MethylDackel (https://github.com/dpryan79/MethylDackel) README does a good job of describing mbias, and MethylDackel provides nice tools for identifying biased positions. I'm guessing you will provide something similar in Biscuit in the long term, but in the short term could you add options for which positions to ignore in the top and bottom strand reads when calling SNPs and estimating methylation?
The MethylDackel (https://github.com/dpryan79/MethylDackel) README does a good job of describing mbias, and MethylDackel provides nice tools for identifying biased positions. I'm guessing you will provide something similar in Biscuit in the long term, but in the short term could you add options for which positions to ignore in the top and bottom strand reads when calling SNPs and estimating methylation?