emeraLD

Tools for rapid on-the-fly LD calculation

About

• 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

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

Software References

Libraries and resources used or adapted in emeraLD:

• Data structures: Boost C++ libraries
• Python Integration: pybind11, pybind dev team
• Tabix and HTSLIB: tabixpp, ekg et al. and htslib, samtools team

Contributors

Special thanks to Daniel Taliun and Ryan Welch

Citation

• To cite emeraLD, you can use Quick et al. (2018) Bioinformatics.

Feedback and bug reports

• Feel free to contact Corbin Quick (corbinq@gmail.com) with bug reports or feedback