emerald¶

Description¶

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.

Environment Variables¶

HPC_EMERALD_DIR - installation directory
HPC_EMERALD_BIN - executable directory

Additional Usage Information¶

sh example.sh

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

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.

Categories¶

biology