# Variant Analysis

Variations in nucleotide sequence, in the form of single nucleotide variants (SNVs) and insertion and deletion events (INDELs), can either be neutral in nature or can have functional effects. Connected Multiomics provides all the tools necessary to interrogate and prioritize variants for further analysis. Variants stored in Variant Call Format (vcf) files can be analyzed to filter, annotate, summarize, visualize, and validate your panel of identified variants. Multiple vcf processing tools are available under the *Variant analysis* section of the context sensitive menu.

* [Annotate Variants](/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants.md)
* [Annotate Variants (SnpEff)](/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-snpeff.md)
* [Annotate Variants (VEP)](/icm/analyses/analysis-functionality/task-menu/variant-analysis/annotate-variants-vep.md)
* [Filter Variants](/icm/analyses/analysis-functionality/task-menu/variant-analysis/filter-variants.md)
* [Summarize Cohort Mutations](/icm/analyses/analysis-functionality/task-menu/variant-analysis/summarize-cohort-mutations.md)
* [Combine Variants](/icm/analyses/analysis-functionality/task-menu/variant-analysis/combine-variants.md)
* [Remove Background Mutations](/icm/analyses/analysis-functionality/task-menu/variant-analysis/remove-background-mutations.md)


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