Canonical Location To Download Genome Annotations

Question

[Drio]

I typically use snpeff to annotate my snps and other genomic variations. The author keeps a very good list of databases up to date but it seems the latest version for this genome is not available. I was in the process of building one but the only place where the data is available is in UCSC (?). The problem is that the data is not in the format required by snpeff.

Before attempting to build the database from UCSC I wanted to ask here if someone else has been in this situation before.

Specifically, my questions are:

1. Is it really UCSC the only place to find this version of the genome and its annotations?
2. If it is, the author of snpeff seems to discourage the creating of databases from this sources. What alternatives do I have in this situation?

And, this is a more broad question but, what is the policy regarding how new data is spread across different sites (ucsc, ensembl, ncbi... ). It seems rather inconsistent to me. Does that data gets at some point synced between sites?

-drd

Answer 1

[brentp]

In the instructions here: http://snpeff.sourceforge.net/SnpEff_manual.html#databases the author does tell how to use refGene tables. It seems to be discouraged because the format changes (not sure how that is).

Since UCSC is your best source for that genome, I'd give it a try following those instructions. The downloads page is here: http://hgdownload.cse.ucsc.edu/goldenPath/papAnu2/database/