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tonydisera / gene.iobio

An iobio app for examining gene variants
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Add pLI values from ExAC to gene information #581

Open mvelinder opened 7 years ago

AlistairNWard commented 7 years ago

  1. There is a directory associated with ExAC (ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint) that contains files with gene level info including the pLi score. There are READMEs to explain them as well, and we should look at the other available metrics.

  2. Also, we should add pLi as a row in the Rank Variants, maybe above VEP.

  3. Might also be nice to add another filter that is for variants in variant intolerant genes.

I would also propose we have a chat about this. We may want to display some gene level info front and centre, so maybe would be worth thinking about how we would build this into the UI - and also what these updates would take to implement and how Tony feels about including them. We have promised that we'll finish off the current plans and let Tony move to something new.

mvelinder commented 6 years ago

I continue to think about this feature. The new gene information panel next to the ranked variants table could be an excellent place to put this information. Let's try to discuss or think about implementing this.

mvelinder commented 6 years ago

@AlistairNWard @tonydisera After talking with more people at CSHL I think we really need to bring these pLI scores into the new vue version of gene. It gets at the lack of burden tests (although not necessarily being a burden score per se) with a strong and accepted metric.

Even if it's just finding a way to fetch the value from the ExAC page. For example: http://exac.broadinstitute.org/gene/ENSG00000104067 with a pLI of 1.0

tonydisera commented 6 years ago

Cool. I will look into how to pull in the pLI score from ExAC.