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BEDFiles.jl

Routines for reading and manipulating GWAS data in .bed files

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Data from Genome-wide association studies are often saved as a PLINK binary biallelic genotype table or .bed file. To be useful, such files should be accompanied by a .fam file, containing metadata on the rows of the table, and a .bim file, containing metadata on the columns. The .fam and .bim files are in tab-separated format.

The table contains the observed allelic type at n single-nucleotide polymorphism (SNP) positions for m individuals.

A SNP corresponds to a nucleotide position on the genome where some degree of variation has been observed in a population, with each individual have one of two possible alleles at that position on each of a pair of chromosomes. Three possible types can be observed are: homozygous allele 1, coded as 0x00, heterzygous, coded as 0x10, and homozygous allele 2, coded as 0x11. Missing values are coded as 0x01.

A single column - one SNP position over all m individuals - is packed into an array of div(m + 3, 4) bytes (UInt8 values).

Installation

This package requires Julia v0.7.0 or later, which can be obtained from https://julialang.org/downloads/ or by building Julia from the sources in the https://github.com/JuliaLang/julia repository.

The package has not yet been registered and must be installed using the repository location. Start julia and use the ] key to switch to the package manager REPL

(v0.7) pkg> add https://github.com/dmbates/BEDFiles.jl.git#master
  Updating git-repo `https://github.com/dmbates/BEDFiles.jl.git`
  Updating registry at `~/.julia/registries/Uncurated`
  Updating git-repo `https://github.com/JuliaRegistries/Uncurated.git`
 Resolving package versions...
  Updating `~/.julia/environments/v0.7/Project.toml`
  [6f44c9a6] + BEDFiles v0.1.0 #master (https://github.com/dmbates/BEDFiles.jl.git)
  Updating `~/.julia/environments/v0.7/Manifest.toml`
  [6f44c9a6] + BEDFiles v0.1.0 #master (https://github.com/dmbates/BEDFiles.jl.git)
  [6fe1bfb0] + OffsetArrays v0.6.0
  [10745b16] + Statistics

Use the backspace key to return to the Julia REPL.

Please see the documentation for usage.