Understanding Variant Calling: VCF Format Explained

What is VCF?

The Variant Call Format (VCF) is a text file format (likely compressed as .vcf.gz) used to store gene sequence variations. It contains a header (metadata) and data lines (variants).

Key Columns

• CHROM/POS: Location of the variant.
• ID: Unique identifier (e.g., rsID from dbSNP).
• REF/ALT: The reference base and the alternative observed base.
• QUAL: Phred-scaled probability that the variant holds.
• INFO: A semicolon-separated list of additional information (e.g., DP=Depth, AF=Allele Frequency).

Common Tools

Tools like bcftools and vcftools are used to manipulate VCFs—filtering, merging, and intersecting variant sets.