https://github.com/illumina/akt
Ancestry and Kinship Tools
https://github.com/illumina/akt
Last synced: 2 months ago
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Ancestry and Kinship Tools
- Host: GitHub
- URL: https://github.com/illumina/akt
- Owner: Illumina
- License: gpl-3.0
- Created: 2016-03-31T16:04:17.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2022-11-16T13:09:54.000Z (over 2 years ago)
- Last Synced: 2025-03-24T07:07:27.707Z (3 months ago)
- Language: C++
- Size: 41.4 MB
- Stars: 70
- Watchers: 10
- Forks: 13
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Changelog: Changelog.md
- License: LICENSE
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README
# akt - ancestry and kinship toolkit
Copyright (c) 2018, Illumina, Inc. All rights reserved. This software is not commercially supported.
Ancestry and Kinship Tools (AKT) provides a handful of useful statistical genetics routines using the [htslib](http://www.htslib.org/) API for input/output. This means it can seamlessly read BCF/VCF files and play nicely with [bcftools](http://samtools.github.io/bcftools/bcftools.html).
Please cite the [AKT paper](https://academic.oup.com/bioinformatics/article-abstract/33/1/142/2525685) if you find this software useful.
## License and dependencies
AKT is freely available under the [GPL3 license](https://github.com/Illumina/agg/blob/master/LICENSE).
AKT relies on HTSlib and Eigen. [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) is a header-only library for matrix algebra released under the [MPL2 license](https://www.mozilla.org/en-US/MPL/2.0/). [HTSlib](http://www.htslib.org/) is a library for efficently parsing vcf/bcf files released under the [MIT/Expat License](http://choosealicense.com/licenses/mit/). Both libraries are included with AKT.
## Installation instructions
```
git clone https://github.com/Illumina/akt.git
cd akt/
make
```
If you get a warning about 'omp.h not found' (especially on OSX)
you can try
```
make no_omp
```
Everything will be run on a single thread, so the `-n` option does nothing
in `akt kin` and `akt ibd`.
## Quick start
akt uses the syntax
```
./akt COMMAND
```
To see a list of available functionality use:
```
Program: akt (Ancestry and Kinship Tools)
Version: v0.3.9-33-g2f4bfea
Copyright (c) 2017, Illumina, Inc. All rights reserved. See LICENSE for further details.
Usage: akt [options]
pca principal component analysis
kin calculate kinship coefficients
relatives discover pedigrees
unrelated generate a list of unrelated individuals
pedphase Mendelian transmission phasing for duos/trios
```
Some useful routine analyses (assumes you are in the akt directory):
```
#Do a PCA:
./akt pca -R data/wgs.grch37.vcf.gz input.bcf > pca.txt
Rscript scripts/pca.R pca.txt
#Project samples onto 1000G principal components
./akt pca -W data/wgs.grch37.vcf.gz input.bcf > 1000G.pca.txt
Rscript scripts/1000G_pca.R 1000G.pca.txt
#Calculate some (robust) kinship coefficients
./akt kin -R data/wgs.grch37.vcf.gz -M 1 input.bcf > kinship.txt
#give me duplicated sample pairs:
awk '{if($6>.4) print $0}' kinship.txt
#reconstruct pedigrees:
akt relatives kinship.txt -p pedigree
#give me a list of unrelated samples
akt unrelated kinship.txt > unrelated.ids
```
Full documentation is available at [http://illumina.github.io/akt](http://illumina.github.io/akt).