The Variant Call Format (VCF) is the emerging standard for storing variant data. Originally designed for SNPs and short INDELs, it also works for structural variations. VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome.

BCF, or the binary variant call format, is the binary version of VCF. It keeps the same information in VCF, while much more efficient to process especially for many samples. The relationship between BCF and VCF is similar to that between BAM and SAM.