Question: annotation issues with ANNOVAR
gravatar for rgambhir
3.6 years ago by
United States
rgambhir10 wrote:

Hi All,

I am trying to annotate a Vcf file that I generated using the VarScan. I could visualize this file on the IGV but I am not able to annotate it using the ANNOVAR. I am not sure what is the problem. Appreciate your help



software error • 1.2k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by rgambhir10
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If working on Galaxy Main at http://usegalaxy,org, the reference genome must be "hg19" if the data is human.

Other genomes supported by the Annovar tool (indexed by the tool authors) can be downloaded and used with the tool on a local or cloud Galaxy. The tool and data manager are in the Tool Shed

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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