> Note that SNPs have around 50 to 150 base pairs of nucleotides
What does this mean? SNPs being, by definition, single nucleotide polymorphisms, how does the author jump from 1bp to 50-150bp? Or is he referring to the surrounding DNA region?
What does this mean? SNPs being, by definition, single nucleotide polymorphisms, how does the author jump from 1bp to 50-150bp? Or is he referring to the surrounding DNA region?
[1]: https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
But that's not a SNP, then, that's a read that happens to contain a SNP.
Generally a SNP is addressed by giving the reference base, the mutated base, the chromosome, the base position in that chromosome, and the assembly used to align the read to that location. For example, a T->C mutation at chr2:25164877 using hg38.
Yes, you need to have the whole read to align to your genome assembly to detect the SNP. But before you do that, you don't know whether you have a SNP. And after you do that, the rest of the read is not useful if what you care about is the SNP.
From the context of the article it's pretty clear that the author was talking about the fragment sizes needed for analysis.
I have a graduate degree in bioinformatics and have worked in the industry for close to a decade, I have a strong background in the exact topic, yes.
Alternately, they're talking about their sequencing reads and calling them SNPs.
I think I should just chalk this one up to my own personal Gell-Mann amnesia and let the article authors do their thing.