Question: Annovar hg38 databases
0
gravatar for clizama
9 weeks ago by
clizama0
clizama0 wrote:

Hey,

I was doing a tutorial For SNP detection. I was using the freebayes and VCFfilter using hg19 like a reference genome first and then I did the same analysis using hg38 like reference genome when I tried to annotate the VCF file with Annovar using hg19 like reference genome all was ok, however when I tried to annotate the file with hg38, the annovar didnt show me the databases. I was wondering if has anyway to setup the databases in galaxy for annovar in order to be able to annotate the vcf files with hg38 reference genome?

Thanks Carlos

snp galaxy annovar • 113 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by clizama0
0
gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

At the public server Galaxy Main https://usegalaxy.org, the human genome Annovar is configured for is hg19. There are no plans to update to hg38 at this time.

Tutorials sometimes use older tools/data. When doing your own analysis, you'll need to decide if using a public server or setting one up of your own. Hg38 annotation is available and could be installed in your own local/docker/cloud Galaxy. Instructions for how to do the configuration is included in the tool repository in the Main ToolShed: https://toolshed.g2.bx.psu.edu/view/saskia-hiltemann/annovar/f7ff063c738e

Galaxy Ecosystem: https://galaxyproject.github.io/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for clizama
9 weeks ago by
clizama0
clizama0 wrote:

Thanks Jen

Carlos

ADD COMMENTlink written 9 weeks ago by clizama0
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