admix-kit 0.1

Tool kits for analyzing genetics data of admixed population

admix-kit

admix-kit is a Python library to facilitate analyses and methods development of genetics data from admixed populations.

admix-kit is currently in beta version and frequently updating. We welcome any feature requests or bug reports. Please ask us "Can admix-kit do XX?". There is chance that some function has already been implemented but not well documented. We can prioritize more useful work if you let us know.

Installation

# Install admix-kit with Python 3.7, 3.8, 3.9
git clone https://github.com/KangchengHou/admix-kit
cd admix-kit && pip install -e .

Installation requires cmake version > 3.12. Use cmake --version to check your cmake version. Use pip install cmake to install the latest version.

In some cases, admix may not be automatically to your $PATH (e.g., because of user installation mode). You need to look through the log and find where admix script is installed to and manually add that to your $PATH (e.g., type PATH=$PATH:~/.local/bin).

To specify a version of admix-kit, use git clone https://github.com/KangchengHou/admix-kit --branch v0.1, or replace v0.1 to other versions listed in https://github.com/KangchengHou/admix-kit/releases.

Get started

• Full documentation
• Quick start (Python)
• Application: Genetic correlation across local ancestry
• Application: GWAS in admixed populations

Use cases

The following manuscripts contain more motivation and details for functionalities within admix-kit:

1. Admix-kit: An Integrated Toolkit and Pipeline for Genetic Analyses of Admixed Populations. bioRxiv 2023
2. Impact of cross-ancestry genetic architecture on GWASs in admixed populations. AJHG 2023
3. Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals. Nature Genetics 2023
4. On powerful GWAS in admixed populations. Nature Genetics 2021