Hello,
*First option* is the tool " SnpEff Variant effect and annotation". This
would require setting up a cloud instance and adding the appropriate
annotation to the tool for use with the genome you are working with. See
the tool shed for more about SnpEff, or the Main/Test server if you want
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.
http://wiki.galaxyproject.org/Cloud
*The second* *option* is to do this in a more step-by-step method,
something like:
1 - start with a pileup file (not vcf, so use Generate pileup, or use
Mpileup without 'Genotype Likelihood Computation:'
2 - use 'Filter Pileup' and for 'Convert coordinates to intervals?:'
choose "yes"
3 - now that the data is in interval format, it can be compared with any
other interval (bed, etc.) dataset that is mapped to the same genome to
determine overlap using the tools in the 'Operate on Genomic Intervals'
tool group.
Obtain gene (actually transcript) annotation bed files ('bed' is a
stricter form of 'interval' format) from sources under "Get Data". Good
choices are UCSC and Biomart for many genomes, in particular because you
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 beta
status on the Test server. You can run it here on very small datasets to
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 statistics
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,
Best,
Jen
Galaxy team
On 8/28/13 10:49 PM, Yan He wrote:
Dear galaxy-users,
I am working on a project to identify and genotype SNPs in targeted
genes. I did some analysis using Galaxy. First, mapping to the genome
with Bowtie. Second, identify SNPs using MPileup in SAMtools. When I
got the pileup file, the SNP information is in which chromosome and
what position. I would like to focus on the SNPs within genes. How
could I extract the SNP information for each genes (SNP position,
coverage)? //Is there a tool in Galaxy to fulfill this? Any help is
highly appreciated!
Best wishes,
Yan
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