Allele-Specific analysis for human WGBS data
I need to perform allele-specific methylation analysis for human whole genome bisulfite sequencing data. As Allele-specific analysis is dependent on SNPs/Polymorphic sites, I stuck with two queries:
- Is there a way to get these polymorphic sites from WGBS data ? (I don’t have any other data for these samples, I mean no exome or WGS to call variants). Has anybody tried using BS-SNPer? I also thought to use SNPs from public sources but it might not be able to resolve two parental alleles as both parents may be heterozygous for the same polymorphisms and it is difficult to tag allele to either mother or father.
- Can allele-specific analysis possible on single sample without the data of parents?
Any suggestions would be helpful.
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