Question: Is it possible to call variants (SNPs) with bisulfite data?
3
gravatar for igor
3.2 years ago by
igor9.1k
United States
igor9.1k 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 • 1.4k views
ADD COMMENTlink modified 3.2 years ago by Devon Ryan93k • written 3.2 years ago by igor9.1k
3
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k 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 3.2 years ago by Devon Ryan93k

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

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by igor9.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1639 users visited in the last hour