skyclub3 / akt

Ancestry and Kinship Tools

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 API for input/output. This means it can seamlessly read BCF/VCF files and play nicely with bcftools.

Please cite the AKT paper if you find this software useful.

License and dependencies

AKT is freely available under the GPL3 license.

AKT relies on HTSlib and Eigen. Eigen is a header-only library for matrix algebra released under the MPL2 license. HTSlib is a library for efficently parsing vcf/bcf files released under the MIT/Expat License. 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 <options>

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 <command> [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.