[GET-dev] Re: Latest draft

[Madeleine Price Ball]

On Sun, May 30, 2010 at 1:28 PM, Xiaodi Wu <xiaodi.wu at gmail.com> wrote:
> Hi Madeleine,
>
> I can commit the change for bug 39 (BLOSUM100) if you update me on
> what the new workflow is in terms of the git repository that's the
> current master, etc. It takes only a few minutes and I may as well do
> it, since I've worked on the original.

I believe this one is the master:
http://github.com/tomclegg/trait-o-matic/

> Re: your comment in bug 22
> (amino acid positions), refFlat does have splice variants. Your best
> bet as to figuring out where the problem is is by double checking to
> see if the SNP has been re-mapped. With every version of dbSNP (and,
> obviously, every major release of the reference genome, but that's not
> what we're interested in here), some of the SNP rs number--genome
> position correlations are changed to reflect better data. This might
> be one of those cases. Otherwise, it's hard to believe how amino acid
> 1891 and amino acid 4399 could be confused; the alternative is that
> they are not and really do point back to the same genome position, in
> which case Trait-o-matic is designed to detect and look up both.

Well, there aren't any splice variants for this produced by
trait-o-matic, we checked that. When I look up the SNP on dbSNP:
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs3798220

I don't know how dbSNP would cause the problem, but I don't think
that's the issue. I find the same position for 36.3 reference genome
build as in the P0 trait-o-matic output, chr6 160881127.

Maybe someone needs to sit down with the refFlat file and figure out
whether it matches UCSC annotation and whether those match the 4399
position published.