Fast calculation of LD in large-scale cohorts¶

Tomahawk is a machine-optimized library for computing linkage-disequilibrium from population-sized datasets. Tomahawk permits close to real-time analysis of regions-of-interest in datasets of many millions of diploid individuals on a standard laptop. All algorithms are embarrassingly parallel and have been successfully tested on chromosome-sized datasets with up to 10 million individuals.

Tomahawk uniquely constructs complete haplotype/genotype contigency matrices for each comparison, perform statistical tests on the output data, and provide a framework for querying the resulting data.

CLI Commands¶

Command	Description
`aggregate`	data rasterization framework for `TWO` files
`calc`	calculate linkage disequilibrium
`scalc`	calculate linkage disequilibrium for a single site
`concat`	concatenate `TWO` files from the same set of samples
`import`	import `VCF`/`VCF.gz`/`BCF` to `TWK`
`sort`	sort `TWO` file
`view`	`TWO`->`LD`/`TWO` view, `TWO` subset and filter
`haplotype`	extract per-sample haplotype strings in `FASTA`/binary format
`decay`	compute LD-decay over distance