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
git clone https://github.com/statgen/emeraLD.git
cd emeraLD
make - 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
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
Special thanks to Daniel Taliun and Ryan Welch
- To cite emeraLD, you can use Quick et al. (2018) Bioinformatics.
- Feel free to contact Corbin Quick (corbinq@gmail.com) with bug reports or feedback