Correcting methylation calls in low-mappability regions

DNA methylation is an important component in vital biological functions such as embryonic development, carcinogenesis, and heritable regulation. Accurate methods to assess genomic methylation status are crucial to its effective use in many scenarios, especially in the detection and diagnosis of disease. Methylation aligners, such as Bismark and bwa-meth, frequently assign MapQ values to reads which are significantly higher than can be supported by the uniqueness of the region they are mapped to. These incorrectly high MapQs result in inappropriate methylation calling in repetitive regions. We observe reads that should map to separate locations (possibly having different methylation states) actually end up mapping to the same locus, causing apparent mixed methylation at such loci.  Methylation calling can be improved by using Bismap mappability data to filter out insufficiently unique reads. Simply filtering out Cs in insufficiently unique regions is not adequate as it is prone to overfiltering Cs in small mappability dips. These Cs can be called using reads anchored in a nearby mappable region. We have created a patch for the MethylDackel methylation caller to perform read-based filtering based on these anchors.  We modified the MethylDackel tools to accept a bigwig file containing a set of regions that are insufficiently unique to place reads accurately. We also enabled an option to allow the user to specify a number bases of overlap with a high quality region for a read pair to be considered during calling.