Overview

Admix-kit is an integrated toolkit for analyzing admixed genotypes and studying genetic effects of complex traits. Here we provide an overview of the package to help you navigate the different components of this package.

Navigate the documentation

We prepare an example simulated dataset (see admixed genotype simulation). We provide example workflows for basic statistics and visualization, local ancestry-aware GWAS, genetic correlation estimation, and polygenic scoring. You can find details about python API and command line interface.

To perform these analysis on your own dataset, please first follow data preparation steps to format your dataset that admix-kit accepts. Then you can similarly apply the above workflows to your own data.

Analysis components

We provide an overview of analyses one can perform with admix-kit. We provide some total time estimates based on our experience in analyzing 20K individuals with ~1M genome-wide HapMap3 SNPs using a machine with Intel Xeon 2.30GHz CPU and 64GB memory. Most of the analyses can be run in parallel in a cluster environment by dividing the genomes into regions (e.g., chromosomes). See each page in details.

Task	Total computing time	Example	Reference
Dataset preparation	2 hours	Guide	-
Local ancestry inference with RFmix	5 hours	Guide	-
Genotype simulation	5 hours	Guide	-
Association testing	10 hours	Notebook	CLI / API
Genetic correlation estimation	30 hours	Notebook	CLI
Polygenic scoring	2 hours	Notebook	CLI / API