I have a dante labs dataset that I would like to cross reference with SNPedia but I am unclear about orientation. I've read the info on SNPedia and other places about it but I just don't get it yet. I realise this is my own stupidity, the explanations feel sound but they seem to be missing some key info that I can't find anywhere.
Anyway without being too tl;dr about what confuses me, I wonder if my dante vcf file has the orientation problem or not because it shows what the reference genome base is next to the sample base. So for example:
1 36571920 rs96067 G A
Chr:1, Pos: 36571920, rsid:rs96067, reference base:G, sample base: A, (another field later in the line defines that both bases are the alt base so this is an (A;A) where the reference had (G;G)).
On SNPedia the genotypes mentioned for rs96067 are C;C, C;T and T;T. Since the reference base in my dante file is a G, which does not show up as a possible reference base on the SNPedia page, does this mean that the dante file is flipped with respect to this gene compared to SNPedia and so I should flip one or other if I want to compare them (flip the base in my file or the data from SNPedia that is)? So I guess flip G->C and A->T meaning my AA becomes TT?
BTW what confuses me about the SNPedia explanation about orientation is this:
Unfortunately if this was instead a SNP where the two alleles are A or T the same flipping logic falls down. We don't (yet) have a way to know for sure if you should be flipped or not, since both forms of your flip rs1234(A;A) and rs1234(T;T) are possible.
Why is AA not the same as TT in this case? Surely this just reflects the direction that the bases were read from, so detection of an AA implicitly means that if we had read from the other direction we would have read TT? I appreciate this is wrong but I don't understand why.
@terdon: Re where I was quoting from, https://www.snpedia.com/index.php/Ambiguous_flip (https://www.snpedia.com/index.php/Orientation also has some info). I've been taking 'flip' as their word for inversion. Re the 'orientation problem' I meant the ambiguity re orientation mentioned in those pages. However you mentioned in your comment that the convention is to always use the + strand. I read up about that and understand now that VCFs use that convention, which answers my question (thanks!). Dbsnp states that it always uses +ve. So like can be compared with like, as long as you use SNP definitions for the correct reference build that your individual SNP VCF has been generated from, and you are using dbsnp as your database. The so called 'flipping' can happen between reference versions/builds and could trip you if you don't use the correct one. Thats what I have gathered to this point, do let me know if its not right.
On SNPedia however many rsid's seem to be defined as minus orientation. They have 2 fields, orientation and stabilised orientation. To quote from the above linked pages:
Orientation indicates the orientation reported in the most current build (currently GRCh38), which is reported below the genotypes in the Reference field. The chromosome number and nucleotide position in that reference build is shown next. StabilizedOrientation is the orientation that is relevant to the genotypes that have been defined in SNPedia for each SNP...
So they are saying that GRCh38 has both plus and minus orientation within and each genotype includes an orientation field? How does this fit with the standard '+ve' convention you mentioned? Maybe these are 2 different things and I just misunderstand. But it would seem far more sensible to simply adjust GRCh38 to all +ve. Is this 'orientation problem' just SNPedias problem? What exactly do they mean on the above linked pages on orientation and ambigous flips?
SNPedia seems pretty useful if it can be made to work - there is lots of associated data on each genotype page, the API is easy to use including for agregated queries etc, but it seems way less reliable than dbsnp despite apparently simply taking their data from dbsnp. Taking the above example I mentioned, rs96067 G>A, dbsnp defines this well, for GRCh37 it shows NC_000001.10:g.36571920G>A. There is also a 'COL8A2 RefSeqGene NG_016245.2:g.23766C>T' entry which I don't fully understand. However on SNPedia as I said all that shows up are C;C, C;T and T;T genotypes. Maybe they are referring to the COL8A2 C>A entry on dbsnp - or did they scrape this SNP def badly? Or are they showing transcript change rather than genomic as Ram RS suggested?