[GET-dev] Mapping build 37 SNPs to build 36 genomes?

Alexander Wait Zaranek awaitz at post.harvard.edu
Fri Jun 18 18:30:36 EDT 2010

> (1) GET-Evidence should be more careful to link to the data set that
> actually has the variant (rather than linking to all current data sets for
> that variant).
> (2) Trait-o-matic should be able to display both data sets publicly, without
> having both appear on the "public samples" front page.
> (3) GET-Evidence should remove the "genome X" sections when a public data
> set becomes non-public (basically "stop linking to a previously public data
> set" is not automated so it's no big surprise that this didn't happen
> properly).  IIRC it does correctly handle "public data set is recomputed and
> no longer has variant V" so it might not take much to fix this.
What we've all been discussing but hasn't crystallized into a plan is
that GET-Evidence should only need to consider genomes in a "PGP
standard genome format".   A different program, let's call it
"Genomerator", should combine all available data sets into "PGP
standard genome format" for consumption by GET-Evidence (and other
applications.)   GET-Evidence, in that scenario, should still be able
to tolerate updates to an individual's data but in the new "standard"

Let's talk further?


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