Emerald

Description

emerald website  

Tools for rapid on-the-fly LD calculation.

Exploits sparsity and haplotype structure to efficiently calculate LD

Uses tabix indexes to support rapid querying of genomic regions

Supports VCF (phased or unphased) and M3VCF formats

Supports integration with Python and R

Environment Modules

Run module spider emerald to find out what environment modules are available for this application.

System Variables

• HPC_EMERALD_DIR - installation directory
• HPC_EMERALD_BIN - executable directory

Performance

sh example.sh

example command: bin/emeraLD -i example/chr20.1KG.25K_m.m3vcf.gz --region 20:60479-238197 --out example

emeraLD v0.1 (c) 2018 corbin quick (corbinq@gmail.com)

reading from m3vcf file...

processed genotype data for 5008 haplotypes...

calculating LD for 1989 SNPs...

done!! thanks for using emeraLD

real 0m1.145s user 0m1.036s sys 0m0.023s

Citation

If you publish research that uses emerald you can cite Quick et al. (2018) Bioinformatics.