[GET-Editors] Questions about assemblies and other interface stuff

Mary Mangan mmangan at openhelix.com
Tue Jul 24 10:42:07 EDT 2012

Hi folks--

I was reading the recent paper, and checking around the GET-Evidence pages, and I have a bunch of questions that I couldn’t resolve with the documentation. I’m sorry if I missed it, but I really did check there first—I swear .

These could be separate items if you want to do them as separate threads. I don’t know what the culture here is yet. But I’ll put them all in this starter email and we can decide how to tackle them.

*One of the things I found really challenging was determining which assembly a variant referred to. For example, on this page http://evidence.personalgenomes.org/FLG2-S2377X there are 2 locations for this variant. I think I might have figured it out from some of the stuff below, but sometimes it’s not as obvious on this. How can I tell on a report page which assembly is referred to?

*For pages like that, with multiple entries for 1000 Genomes, what subsets of 1000G are we talking about? I couldn’t figure out what different 1000Gs meant.  Related to this, which HapMap release are we talking about on pages with HapMap? Are the EVS releases that matter?

*Impact scores: I was trying to understand these and wanted to read this page, but it was 404: http://evidence.personalgenomes.org/guide_impact_scores

*Everything I found was labeled by amino acid change, according to this, I get that: http://evidence.personalgenomes.org/guide_amino_acid_calls  But again, I can’t tell what coordinate system is the framework here—which assembly? Which protein is the source of the coordinates?

*Is there a way to locate variants that aren’t associated with a gene/protein? I couldn’t figure that out. I understand from the documentation that’s the focus, but I am interested in promoter regions, for example. Any way to get there?

So those are some initial questions. Thanks for any guidance.


Mary Mangan, PhD
OpenHelix LLC
twitter @openhelix
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