variant-analysis-tools

What problem does it solve?

This Skill provides a streamlined process for analyzing variant call files (VCF/BCF), enabling users to summarize, filter, and triage genetic variants locally before complex downstream analysis.

Core Features & Use Cases

• Variant Summarization: Get counts of SNVs, indels, and structural variants.
• Filtering: Apply filters based on variant allele frequency (VAF), read depth, PASS status, and consequence.
• Gene/Consequence Triage: Identify top affected genes and filter out specific variant consequences (e.g., intronic).
• Use Case: Inspect a VCF file to count mutation classes, filter variants with a VAF below 5%, and summarize the top affected genes.

Quick Start

Run the variant report script to analyze 'cohort/sample.vcf.gz' for the 'TUMOR' sample, keeping only PASS variants with a minimum VAF of 0.05 and depth of 20, excluding intronic consequences, and saving the output to 'variants/sample_filtered.csv' and 'variants/sample_filtered.json'.