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Question: Which tools can be used for gene annotation and for determining zygosity?
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gravatar for debanjan.roy12
6 months ago by
debanjan.roy12 • 0
debanjan.roy12 • 0 wrote:

I am unable to find VCFannotate tool in Galaxy and if I am using AnnovarAnnotate I am only getting an empty output with headers. Is there any tool alternative to VCF Annotate for gene annotations?

Also, is there a tool that can provide the information about whether a mutation is homozygous or heterozygous?
annotation variant annovar vcf galaxy • 270 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by debanjan.roy12 • 0
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gravatar for joshigaurav0007
6 months ago by
joshigaurav0007 • 10
joshigaurav0007 • 10 wrote:

You can refer the following link. https://galaxyproject.org/tutorials/var_dip/
ADD COMMENT • link written 6 months ago by joshigaurav0007 • 10

Note: Annovar's annotation indexes are only installed for the database hg19 at Galaxy Main https://usegalaxy.org.

Alternatives are in the tutorial above with more options under the tool groups NGS: Variant Analysis, NGS: Gemini, and NGS: VCF Manipulation (last group contains VCFannotate).

If you are working at another public Galaxy server, the tools available can vary. If working at your own local/docker/cloud Galaxy, these tool and more can be installed from the ToolShed https://usegalaxy.org/toolshed

All Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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