VariantClassifiers

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Contents

Overview

VariantClassifiers have replaced FunctionalAnnotationFiles with clean/curated mutation annotation. The dynamic mutation annotation step is much faster in land based on classifers, compared to FunctionalAnnotationFiles.To visualize variant annotations in Land, the VariantClassifiers option must be defined in the Land.cfg file. Annotations are not defined by default.

For a full description of variant, gene, and region based annotations please see our AnnotateVariants.pdf wiki page.

ArrayLands

We recommend using the following Variant Classifiers if you would like to mimic the Omicsoft OncoLands and DiseaseLands:

VariantClassifiers=ClinVar_20160815,FunctionalMutation_20160815,1000GenomesSimple_20160815,ExAC_20160815,ESP6500_20160815,UK10K_20160815,RegulomeDB_20160815

Adding these parameters to the Land.cfg file will add mutation metadata to the Land. This can be visualized in gene detail views:

Annotation details.png

In this view, users can identify the frequency of the selected mutation, for example in the 1000 Genomes project (broken down by total, and region-specific frequencies)

and also can be used in conjunction with default filters in the Mutation tab to filter mutations based on criteria in these classifiers:

Mutation filters.png

GeneticsLand

Variants in GeneticsLands can be filtered based on a comprehensive list of variant classifiers:

Variantclassifiers.png

AllSNPsVariantClassifier.png

If you would like to request to add a classifier or have an interested in one that we do not currently provide, please contact Omicsoft support for instructions on modifying the [VariantClassifier] option of the GeneticsLand Land.cfg.

If this parameter is updated for a GeneticsLand, all dynamic annotations will be updated when the land is refreshed. Note that users may notice Association views will be slower to load after the initial change to the VariantClassifier paramenter. The stored annotations for the Association.TopHits, Association.GenomePlot, and Association.PValueQQPlot views will be refreshed the next time each view is accessed by the user (may take a few minutes).

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