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Introduction

The primary goal of tomahawk is to efficiently and conveniently compute linkage-disequilibrium for a single site vs its local neighbourhood, a sliding window across an interval, or all-vs-all pairwise genome-wide. Tomahawk is a C++ library with a standard CLI divided into various subroutines, as is the standard for most bioinformatics tools.

• tomahawk is much more efficient than existing solutions, both in terms of memory usage and compute time. tomahawk can easily compute genome-wide LD for cohorts of millions of samples over chromosome-scaled regions.

• tomahawk is designed as a C++ API to simplify LD-based workflow: either directly by using the C++ API or using any of the available language bindings. Currently there are R bindings and Python3 bindings.

• tomahawk has its own human-readable (.ld) interchange format and a highly compressed binary (.two) format for expedient analysis of the generated output data. Other text-based systems are extremely inefficient and do not support basic operations such as subsetting, searching, summarizing, and visualizing.

• tomahawk accepts any valid htslib-compatible input variant call format file for import into the internal binary tomahawk (.twk) file format.