Is it possible to call variants (SNPs) with bisulfite data?

Question

[igor]

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.

Answer 1

[Devon Ryan]

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.

[igor]

I was hoping there was a trick to use existing variant callers, but thank you for the suggestions. Biscuit seems promising.