EasyLD.jl

This is a Julia package that helps users download and read blocks of LD (linkage disequilibrium) matrices stored as Hail Block Matrix format into memory. This package is inspired by an existing pipeline curated by Aaron Sossin.

We tested this package for processing the following

1. gnomAD LD matrices
2. Pan-UKBB LD matrices

Installation

This resource uses AWSS3.jl to download files from Amazon servers. Thus, one needs to register an account with AWS first.

To install this package, download Julia. Within Julia, execute the following

using Pkg
pkg"add https://github.com/biona001/EasyLD.jl"

Manual Outline

• API
• • Exported functions
  • Internal helper functions and structs
• Pan-UKB data
• • Downloading
  • Reading LD panel with Matrix interface
  • Read in a block with get_block
  • SNP information
• gnomAD data
• • Downloading
  • Reading LD panel with Matrix interface
  • Read in a block with get_block
  • SNP information