Detecting SNPs or Ambiguous Bases in ABI files programatically with R or Bioconductor

Question

[jnf3769]

I am looking to do some fairly specific QC by looking into the signal information of an abi file. I have the data read into R using sangerseqR and can access the S4 data just fine. What I need to know is how I would detect potential SNPs or ambiguous bases that aren't obvious enough to be caught by the rest of my pipeline. Unfortunately, I need to do this programmatically as part of a larger pipeline I built. An example can be seen here. It isn't such a low quality sequence that QC will catch it, nor is it entirely clear that it is a real SNP (indeed, it shouldn't be based on the nature of the data). I don't need to call the SNP or do anything with it other than remove the sequence from my list of candidates, so a simple, binary detection would be fine. Any clues?

Answer 1

[Lesley Sitter]

I'm not an expert so correct me if I'm wrong but I think you are not able to do SNP detecting with this data.

A SNP is a single nucleotide polymorphism. These SNPs are found by having two samples (wild an query) where the query has a nucleotide that is different from the wild type.

In your case you only have one sample so these are not SNPs. Because I can't see the entire run I can't really determine if the overall quality of that region is lower than other regions (which could indicate just noise). My guess is that these areas are just heterozygous areas and should be called as an N (undetermined nucleotide).

If you want to call SNPs you have to have at least two samples or have a reference genome and you probably want entirely different data than abi files because these are not really informative for those types of analyses.