CT SNP filtering with destranding problem

sartorlab / methylSig

R package for DNA methylation analysis

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CT SNP filtering with destranding problem #2

Closed rcavalcante closed 9 years ago

rcavalcante commented 9 years ago

When filterSNPs=T and destranded=T it is possible for CpG sites +1bp from a CT SNP will be moved back to the CT SNP site in the destranding step. Currently thinking about how to deal with this...

rcavalcante commented 9 years ago

We do not want to include the +1bp from the CT SNP either, because a C > T SNP would mean no CpG methylation on the reverse strand anyhow. This problem is solved by filtering the SNPs after destranding.