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BioJulia/GeneticVariation.jl package, which has been superseded by
- 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
using Pkg pkg"add VCFTools"
This package supports Julia
- Ancestry Informative Markers
- Match markers in two VCF files
- Convert genotype/haplotype/dosage to numeric arrays
- Filter data fields in a VCF file
- Genetic Relationship Matrix
- VCF summary information