Question: Which tools can be used for gene annotation and for determining zygosity?
0
gravatar for debanjan.roy12
12 weeks ago by
debanjan.roy120 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?

ADD COMMENTlink modified 12 weeks ago by Jennifer Hillman Jackson25k • written 12 weeks ago by debanjan.roy120
1
gravatar for joshigaurav0007
12 weeks ago by
joshigaurav000710 wrote:

You can refer the following link. https://galaxyproject.org/tutorials/var_dip/

ADD COMMENTlink written 12 weeks ago by joshigaurav000710

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 REPLYlink written 12 weeks ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 95 users visited in the last hour