bcftools-variant-manipulation

What problem does it solve?

This Skill streamlines the complex process of manipulating variant call files (VCF/BCF), enabling efficient filtering, merging, annotation, and querying of genetic variation data.

Core Features & Use Cases

• Variant Filtering: Apply quality thresholds and flags to retain high-confidence calls.
• Data Extraction: Transform VCF content into tabular text for downstream analysis.
• Annotation: Add identifiers and gene information to variant records.
• Use Case: You have a raw VCF file from a variant caller and need to filter out low-quality variants, annotate them with dbSNP rsIDs, and extract a list of variants with allele frequencies above 1%.

Quick Start

Use the bcftools skill to filter the file 'variants.vcf.gz' to keep only variants with QUAL greater than 20 and DP greater than 10.