akt - ancestry and kinship toolkit

Ancestry and Kinship Tools (AKT) provides a number 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 pre-print 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 Macs) 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:	a963bf1
Copyright (c) 2016, Illumina, Inc. All rights reserved. See LICENSE for further details.

Usage:	akt <command> [options]

	pca                      principal component analysis
	kin                      detect average IBD sharing
	relatives                discover pedigrees
	mendel                   profile Mendelian inhertiance and inconsistencies in known pedigrees
	cluster                  perform cluster analyses
	LDplot                   output correlation matrix
	stats                    calculate AF and LD metrics
	prune                     perorms LD pruning of variants
	tag                      selects a set of K tagging variants
	metafreq                 examine two files for AF differences

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

#Find close relatives/duplicates:
./akt pca -R data/wgs.grch37.vcf.gz input.bcf > kinship.txt
awk '{if($5>.15) print $0}' kinship.txt

#reconstruct pedigrees:
akt relatives -p pedigree kinship.txt

Full documentation is available in docs/usage.md along with a large set of example use cases in docs/examples.md

ramabit/akt

akt - ancestry and kinship toolkit