Calling SNPs from RRBS data
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6.2 years ago
Jautis ▴ 300

Hi, does anybody know of a way to call SNP data from RRBS or another form of bisulfite sequencing? Typical programs to call SNPs have difficulty because RRBS sequences are non-complementary and have mutated base pairs. 

 

The system does not have to be perfect or detect all SNPs; I'm hoping to use the data primarily for mapping local ancestry. 

 

Thank you!

SNP RRBS bisulfite sequencing SNP calling • 2.4k views
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6.2 years ago

Bis-SNP.

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So our lab tried Bis-SNP in the past but it didn't work well. Are there any alternatives out there? 

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Got here a bit late, but just in case someone is still looking for (faster) alternatives,

https://github.com/zwdzwd/biscuit

https://github.com/hellbelly/BS-Snper

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Not that I'm aware of. Calling variants from BSseq data is problematic for a number of reasons, so it's rarely done.

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Makes sense; we're just looking for an option to get population-level SNPs in non-model organisms to go along with RRBS data w/o having to pay for 2 rounds of sequencing

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The best bang for your buck is going to be to just do RRDNAseq, which is an abbreviation I probably just made up for RRBS sans the bisulfite treatment. Given the quality of the many BSseq datasets I've seen, I wouldn't put that much trust in calling variants from them.
 

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