Question: Is it possible to call variants (SNPs) with bisulfite data?
3
gravatar for igor
4.0 years ago by
igor11k
United States
igor11k wrote:

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.

rrbs wgbs • 1.8k views
ADD COMMENTlink modified 4.0 years ago by Devon Ryan97k • written 4.0 years ago by igor11k
3
gravatar for Devon Ryan
4.0 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Devon Ryan97k

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

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by igor11k
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