[BioC] variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?

[Steve Lianoglou]

Hi,

On Tue, Feb 4, 2014 at 6:46 PM, Janet Young <jayoung at fhcrc.org> wrote:
> Hi Valerie,
>
> Thanks for both of these emails.  It's very nice for me that you have implemented these changes already!  It looks like I'll have to wait until tomorrow for version 1.9.34 of VariantAnnotation - I'll definitely try it then.
>
> I'm also taking a look at ensemblVEP now - thanks for the tip.  I actually began this whole mission last week by trying to use the VEP script on my vcf files from the command line.  The script (and the bioconductor wrapper) works fine for me on test human data.  I love all the extra annotations that are available via VEP for human (SIFT, polyphen).

Although this isn't a bioconductor thing, I can't help but point out
this new paper since VEP came up:

A general framework for estimating the relative pathogenicity of human
genetic variants
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2892.html

They also provide precomputed "CADD scores" (something like polyphen
or sift) for "all 8.6 billion possible single nucleotide variants
(SNVs) of the reference genome, as well as all variants from the 1000
Genome and ESP variant releases and enable scoring of short
insertions/deletions."

Thought it might be useful ...

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech