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VCFTools.jl

Julia utilities for handling VCF fiels

VCFTools.jl implements some Julia utilities for handling VCF files. This package heavily uses the VCF parser developed in the BioJulia/GeneticVariation.jl package.

Package Features

• Calculate genotype statistics (minor allele frequencies, minor allele, count of missing genotypes, etc) from a VCF file.
• Extract specific data fields from a VCF file.
• Match markers in two VCF files according to ID.

Installation

Use the Julia package manager to install VCFTools.jl.

Pkg.clone("https://github.com/OpenMendel/VCFTools.jl.git")

This package supports Julia 0.6.

Manual Outline

• VCF summary information
  • Example VCF file
  • Summary statistics
• Filter data fields in a VCF
  • Example VCF file
  • Extract a single field
  • Extract more than one fields
  • No found data fields
• Convert GT to numeric arrays
  • Example VCF file
  • Genetic model
  • Convert GT data into a numeric matrix
  • Extract GT data marker-by-maker or window-by-window
• Match markers in two VCF files
  • Example files
  • Match markers according to ID
  • Match markers according to position
• API
  • Index
  • Functions