What Is The Parent Table For Snp137? (Using Annonvar)

Question

[sandhya0888]

Which is the parent table for snp137?

I am using snp137Nonflagged with Annovar to annotate variables. Which is better to use,the parent table or just the nonflagged?

Answer 1

[Jorge Amigo]

it depends on what exactly you're looking for. the "snp137" table contains all the information stored in UCSC's genome browser from dbsnp's build 137, and the "snp137Nonflagged" table contains a subset of the previous by removing those flagged SNPs (SNPs < 1% minor allele frequency (MAF) (or unknown), mapping only once to reference assembly, flagged in dbSnp as "clinically associated").

here is an example: in our variant detection pipeline we use "snp137" to get the rs codes for all the variants we detect, and we use "snp137Nonflagged" too as an additional annotation that shows us which ones haven't been reported as rare variants (note that not all SNPs have population frequency associated, so some of that "snp137Nonflagged" table may still be rare variants) or that haven't been (yet) associated with any clinical trait.

let me just stress that this "snp137Nonflagged" annotation should be use with caution, because it doesn't tell you which variants can be simply filtered out, but it may be of some help (and you should be the one evaluating the extent of that help) to classify your variant set into more and less relevant. this protocol is very similar to a very extended one years ago, which used snp129 as the reference source of common variation, allowing to split variant sets into common and rare variants, i.e. into known and unknown. as NGS evolves and dbSNP continues growing by accepting new variants, using it as before would be a way of detecting even rarer variants. it is acceptable, but as long as you take everything mentioned before into account.