Is it possible to call variants with WGBS or RRBS data? Since there are many C/T conversions, those would be considered SNPs when they really aren't.
Yes, it's possible, since the strand opposite of C's will be unaffected by bisulfite. A common tool for this is "BisSNP", though it's incredibly slow and I'd probably give biscuit a try first.
I was hoping there was a trick to use existing variant callers, but thank you for the suggestions. Biscuit seems promising.
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