This is an RDF.rb reader plugin for Variant Call Format (VCF) files, widely used in bioinformatics.
Note: at present, the project requires JRuby 9.0 (or newer) due to the Java-based VCF parser. We hope to eventually substitute Bio-vcf instead.
- Implements an RDF.rb reader for VCF and BCF files, supporting also bgzipped files.
- Includes a CLI tool called
vcf2rdfto transform VCF files into RDF.
Reading VCF Files
The gem can be used like any other RDF.rb reader plugin:
require 'rdf/vcf' RDF::VCF::Reader.open('Homo_sapiens.vcf.gz') do |reader| reader.each_statement do |statement| p statement end end
Command-Line Interface (CLI)
The gem includes a CLI tool called
vcf2rdf which transforms VCF files into
RDF (currently, N-Triples):
files can be in plain text or bgzip compressed data
Please create the tabix index by youself, in future this gem will create the index automatically.