Does indel effect the methylation calling or C context determination

dpryan79 / MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

MIT License

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Does indel effect the methylation calling or C context determination #145

Open huichanghuang opened 1 year ago

huichanghuang commented 1 year ago

Hi, Since mapping bam file from bwa-meth does not include an XMtag like Bismark， Is there any way can I know how hpl indel effect the methylation call or C context determination? Thanks. Best regards, Huichang Huang

dpryan79 commented 1 year ago

InDels themselves will be outside of the calls as well as the context, which is taken from the reference sequence.