variant_analysis.md

Variant Analysis Pipeline

This module provides functionality for analyzing genetic variants from VCF files.

Overview

The variant analysis pipeline includes the following steps:

1. Loading VCF files
2. Annotating variants with additional information
3. Filtering variants based on specific criteria (e.g., minor allele frequency)

Main Functions

• load_vcf(file_path): Loads a VCF file into a pandas DataFrame.
• annotate_variants(vcf_df): Annotates variants with additional information.
• filter_variants(annotated_df, maf_threshold=0.01): Filters variants based on minor allele frequency.

Usage

from src.variant_analysis.variant_analysis import main

main("path/to/your/vcf/file")

This will process the VCF file, annotate variants, apply filtering, and output the results.