## Variants / Annotate variants

### Description

This tool annotates the variants in a VCF file.

### Parameters

- Genome (Human (hg38)) [Human (hg38), Human (hg19)]

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Details

Variants are read from a VCF file and assigned to chromosome, genes and transcripts using the Bioconductor package VariantAnotation. Gene symbols, names and Entrez Gene IDs are taken from the organism specific annotation packages generated by the Bioconductor project.

In addition, coding variants are separately treated. Data on coding variants includes their locations in the transcripts and proteins, inferred consequences of the variants, and specific sequences of the codons and the alleles. Gene symbols, names and Entrez Gene IDs are taken from the organism specific annotation packages generated by the Bioconductor project. In additions, for the coding non-synonymous variants, the PolyPhen -predictions are fetched and printed into a table.

### Output

The analysis output consists of the following files:

- all-variants.tsv: Results for all variants in the VCF file.
- coding-variants.tsv: Results for the coding variants in the VCF file.
- polyphen-predictions.tsv: PolyPhen predictions for the non-synonymous coding variants in the VCF file.