An important aspect of variant analysis is the ability to prioritize the variants.  As variant detection can often identify a large number of variants, it may be difficult to determine which variants may impact phenotypes. As implemented in Partek^® Flow^®, the Ensembl Variant Effect Predictor (VEP, version 84)¹ provides a means to add detailed annotation to variants in the project such as discrete aspects of transcript models and variant databases not available in the Annotate Variants task.  For variants identified in human data, information from popular tools that predict the impact of variants that cause amino acid changes, SIFT^2–4 and PROVEAN⁵ (available for the hg19 genome assembly), will be included.  VEP databases can be obtained for multiple species, and content will be dependent on available transcript and variant information for that organism.  The Annotate variants (VEP) 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 the Summarize cohort mutations Cohort mutation summary report.

Annotate variants (VEP) dialog

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