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!
1 answer
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written
by
Devon Ryan
Not that I'm aware of. Calling variants from BSseq data is problematic for a number of reasons, so it's rarely done.
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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written
by
Devon Ryan
Got here a bit late, but just in case someone is still looking for (faster) alternatives,
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