snpeff-variant-annotation

What problem does it solve?

This Skill automates the annotation of genetic variants in VCF files, predicting their functional consequences and enabling filtering for biologically relevant mutations.

Core Features & Use Cases

• Functional Annotation: Predicts the impact of variants (e.g., HIGH, MODERATE, LOW) on genes and transcripts.
• Variant Filtering: Filters VCF files based on impact, allele frequency, and clinical significance.
• Database Enrichment: Adds annotations from ClinVar and dbSNP for pathogenicity and variant identification.
• Use Case: You have a VCF file from a whole-genome sequencing experiment. Use this Skill to identify all HIGH-impact variants that could be pathogenic and then annotate them with their ClinVar status.

Quick Start

Annotate the input.vcf.gz file with SnpEff for the hg38 genome assembly.