GeneticResources / emeraLD

tools to efficiently retrieve and calculate LD

emeraLD

Tools for rapid on-the-fly LD calculation

About

• Exploits sparsity and haplotype structure to enable rapid LD calculation with massive data sets
• Uses tabix indexes to support rapid querying of genomic regions
• Supports VCF (phased or unphased) and M3VCF formats
• Provides easy-to-use R interface to avoid storing/precomputing LD. This can save space without compromising speed for GWAS analysis in R
• In data sets with 10Ks of samples, emeraLD is 5-20x faster than PLINK-1.9 and 100s-Ks of times faster than existing tools for VCF files

Installing

git clone https://github.com/statgen/emeraLD.git  
cd emeraLD  
make  

Usage

• Example usage from command line

# example usage for calculating LD in a region:
bin/emeraLD -i example/chr20.1KG.25K_m.m3vcf.gz --region 20:60479-438197 --stdout | bgzip -c > output.txt.gz

- Example usage from R interface (see emeraLD2R.r file) 
```R
## "$chr" functions as chromosome wildcard 
in_path <- "example/chr$chr.1KG.25K_m.vcf.gz"

## emeraLD2R creates an LD retrieval function 
getLD <- emeraLD2R(path = in_path)

## calling an LD retrieval function invokes emeraLD
ld_data <- getLD(region = "20:83061-92955")
## emeraLD processes genotypes; LD output is passed to R

## check LD output 
head(ld_data$Sigma[, 1:10], 10)
head(ld_data$info)

Feedback and bug reports

• Feel free to contact Corbin Quick ([e-mail]) with bug reports or feedback