An important aspect of variant analysis is the ability to prioritize the specific variants for further investigation.  As variant detection can often identify a large number of variants, it may be difficult to determine which variants may impact phenotypes.  SnpEff (version 4.1k) provides a means to annotate and predict the effects of variants on genes, allowing for prioritization of variants within the project.  In addition, the SnpEff databases utilized for prediction support a large number of genome assemblies.  Information regarding the implementation of the predictions is detailed by Cingolani et al.¹  The predicted effect of the variant is categorized by impact:

• HIGH - frame shifts, addition/deletion of stop codons, etc; 
• MODERATE – codon change/deletion/insertion, etc; 
• LOW – synonymous changes, etc; 
• MODIFIER – changes outside coding regions, etc.  

Further details about output metrics can be found in the SnpEff documentation.  The Annotate variants (SnpEff) task can be invoked from any Variants or Annotated variants data node, and the task will supplement any existing annotation in the vcf files.  Annotation information will also be visible in the View variants Variant report and the Summarize cohort mutations Cohort mutation summary report

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Advanced options provides a means to tune parameters for annotation generated from the SnpEff database.  Upon invoking the task dialog, Option set is set to Default, and these parameters are provided prescribed by the developers of SnpEff developers.  Clicking Configure will open a window to tune advanced options (Figure 2).  SnpEff has Advanced options for Results filter options, Annotation options, and Database options.  Moving the mouse cursor over the info button will provide details for each parameter.

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