*First option* is the tool " SnpEff Variant effect and annotation".
would require setting up a cloud instance and adding the appropriate
annotation to the tool for use with the genome you are working with.
the tool shed for more about SnpEff, or the Main/Test server if you
to try it out - is not set up for very many genomes and quotas on Test
are small, as it is not intended for intensive use.
*The second* *option* is to do this in a more step-by-step method,
1 - start with a pileup file (not vcf, so use Generate pileup, or
Mpileup without 'Genotype Likelihood Computation:'
2 - use 'Filter Pileup' and for 'Convert coordinates to intervals?:'
3 - now that the data is in interval format, it can be compared with
other interval (bed, etc.) dataset that is mapped to the same genome
determine overlap using the tools in the 'Operate on Genomic
Obtain gene (actually transcript) annotation bed files ('bed' is a
stricter form of 'interval' format) from sources under "Get Data".
choices are UCSC and Biomart for many genomes, in particular because
can select out reference bed files that contain specific regions of
transcripts: UTR, Exons, Introns, user-specified regions upstream or
down, etc., but other sources may be appropriate depending on your
genome and needs. As long as the reference annotation you are using is
mapped to the same exact genome, then this will work. Once you have a
process, save it in a workflow for future use.
*Another great (NEW!) option* includes some tools that are still in
status on the Test server. You can run it here on very small datasets
see if you like, then decide if moving to a cloud and setting it up
there is something you want to do. Called "Naive Variant Detector" and
"Variant Annotator", these run on VCF files, and will produce
somewhat similar to (but with more detail and a different underlying
algorithm than) "Filter Pileup". The result here is not in interval
format - it is VCF, but it could converted (use tools in Text
Manipulation to create a start/stop) or proceed to SnpEff as is.
You had another earlier question about this same analysis - I will
include some other advice in that reply, next,