Question: SNPs associated with a gene
gravatar for sara.mehrabi
18 months ago by
sara.mehrabi40 wrote:

Dear All,

which tool is recommended to use for finding out which SNPs associated with which gene? I have the vcf and gtt files.

Thank you.

Best, Sara

snp • 557 views
ADD COMMENTlink modified 18 months ago by Guy Reeves1.0k • written 18 months ago by sara.mehrabi40
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There are a few tools that can add in the annotation. Those that annotate a VCF with gene/transcript annotation will output very similar content, so which to pick will depend on what you want to do with the data downstream (if anything) with the related tools. Perhaps give a few a try then review?

Note: Some will need the reference data provided in BED format. GTF format can be transformed into BED format or extract the content in BED format from the source and/or rearrange it yourself using tools in the group Text Manipulation. The tool forms explain the expected reference data input and/or if the reference data is a built-in index.

See the tool groups:

  • NGS: VCF Manipulation
  • NGS: Variant Analysis
  • NGS: Gemini

Example 1: To just do this operation (add in gene name) from any genome, including a custom genome - VCFannotate is a quick way to add that annotation to the INFO field of the VCF dataset if the reference BED dataset has the gene name in the name field (4th column).

Example 2: To do this operation and potentially more, if your data is from hg19 - ANNOVAR is another quick way to add in this annotation, along with other annotation, in a single step, using built-in indexes. Please be aware that the very latest version of this tool (version 0.2) has some technical issues, so use the prior version (0.1).

Example 3: To do even more (add in gene name, discover predicted functional changes, etc), from a wider range of available genomes - Try the Gemini tool suite if your reference genome is available. There is a tool to check available genomes with indexes, a tool to download the indexes, and several tools to annotate and extract derivative information.

Variant analysis tutorials for Galaxy are here:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
gravatar for Guy Reeves
18 months ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:

HI I would recommend 'SnpEff Variant effect and annotation' widely used and does a great job as long as your genome is available from 'SnpEff Download Download a new database' you will not need your get. Cheers Guy

ADD COMMENTlink written 18 months ago by Guy Reeves1.0k
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