Feature: Variant annotations


Hi everyone,
  This is a pull request for adding an Avro IDL file for variant annotations (annotations.avdl). 
  Annotations include records for variant effect, impact, coding and non-coding information, 
clinical relevance, etc.
  It is heavily based on VEP (ENSEMBL's Variant Effect Predictor) and SnpEff (an annotations 
tool I wrote).

> What's the best link to reference UCSC's transcript set versions?

At this point we don't have a good way to get those, unfortunately.  You can find some version numbers in this list of track releases (most recent first):
http://genome.ucsc.edu/goldenPath/releaseLog.html#hg19
for example, "Ensembl Genes v75" or "GENCODE V19 release"... hmm, for CCDS we have only "Initial CCDS release on GRCh37".  Currently we don't even include dates, ugh... thanks for making me look into that dusty old closet!  If we were to serve up transcript sets for GA4GH we would include a proper version identifier if we have it; if we don't, we could at least provide a create date for our copy of the transcript set.  

I think it would be best to get transcript sets straight from the source (from GENCODE, Havana etc) when possible.