VCFTools.jl

Julia utilities for handling VCF files

VCFTools.jl implements some Julia utilities for handling VCF files. This package heavily uses the VCF parser developed in the BioJulia/GeneticVariation.jl package, which has been superseded by VariantCallFormal.jl

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.
• Filtering/subsetting VCF files.
• Match markers in two VCF files according to ID.
• Calculation of Genetic Relationship Matrix.
• Rank SNPs by their ancestry informativeness.
• Saving numeric matrix into VCF file

Installation

Within Julia,

using Pkg
pkg"add VCFTools"

This package supports Julia v1.5+.

Manual Outline

• VCFTools.jl
• • Package Features
  • Installation
  • Manual Outline
• Ancestry Informative Markers
• • Example data
  • Preprocess data
  • Run AIM selection
• API
• • Index
  • Functions
• Match markers in two VCF files
• • Example files
  • Match markers according to ID
  • Match markers according to position
• Convert genotype/haplotype/dosage to numeric arrays
• • Example VCF file
  • Genetic model
  • Convert GT data into a numeric genotype matrix
  • Convert GT data into haplotypes panels
  • Convert DS data into dosages
  • Extract data marker-by-maker or window-by-window
  • Sample ID, Chromosome, SNP position, REF/ALT alleles
• Filter data fields in a VCF file
• • Example VCF file
  • Extract a single field
  • Extract more than one fields
  • No found data fields
  • Subsetting VCF files using array masks
  • Filter by chromosome
  • Masking entries of a VCF files
• Genetic Relationship Matrix
• • Example data
  • High proportion of missing data
  • Inhomogeneous populations
• VCF summary information
• • Example VCF file
  • Summary statistics
• Write
• • Phased genotypes
  • Unphased genotypes