A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
Fig 2
Example of the VCF format and a VCF transformation to Javascript Object Notation (JSON) using bio-vcf.
(a) the line-based VCF record makes use of separators to split tab-delimited fields into subfields. Subfields are split with characters, =:;/ and so on. This splitting effectively projects a ‘tree-like’ datastructure that can also be represented as (b) a JSON record. JSON is used as a common data exchange format for databases and web-services. This example was generated with (c) the bio-vcf tool using a template [24]. bio-vcf transform data to any textual format, including RDF, HTML, XML etc. See also the bio-vcf section.