NgsAdmix

This page contains information about the program called NGSadmix, which is a very nice tool for estimating individual admixture proportions from NGS data. It is based on genotype likelihoods and works well for medium and low coverage NGS data. It is a fancy multithreaded c/c++ program which makes it useful for large datasets.

The great thing about NGSadmix is that it is a new method that takes the uncertainty introduced in NGS sequencing data into account when inferring an individual's ancestry by using genotype likelihoods that considers the uncertainty caused by unobserved genotypes.

As with the other existing software, ADMIXTURE and STRUCTURE, NGSadmix is only sensitive to admixture recent enough to cause structures in the population in terms of differing allele frequencies. Historical admixture events after which many generations has passed in the population, leaves no signature in terms of systematic differences in allele frequencies between individuals and are not a concern in association studies.

The method was published in 2013 and can be found here: [1]

Software Download

The latest version of NGSadmix is ngsadmix32 from June 25, 2013 and can be downloaded here: [2].

Older Versions

The previous version of NGSadmix, ngsadmix31 can be found here: [3].

Version Log:

• v32 june 25-2013; modified code such that it now compiles on OSX
• v31 june 24-2013; First public version.

Installation

NGSadmix can be installed independently or as a part of ANGSD.

NGSadmix Independent Installation

1. Login to your server using ssh on your terminal window.

2. Create the directory where you will install your software and enter it, such as

mkdir ~/Software

cd ~/Software

3. Download the source code:

wget https://raw.githubusercontent.com/ANGSD/angsd/master/misc/ngsadmix32.cpp

4. Configure, Compile and Install:

g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix

NGSadmix Installation from ANGSD

NGSadmix is part of the package ANGSD. To install ANGSD, please follow the instructions here [4]

Quick start

./NGSadmix -likes inputBeagleFile.gz -K 3 -o outFileName -P 10

• -likes beagle file of genotype likelihoods
• -K number of clusters
• -o prefix of output file names
• -P Number of threads used

Parameters

All parameters are set using -par value. For example, to get additional information, you would write -printInfo 1.

./NGSadmix  

Arguments:

-likes .beagle format filename with genotype likelihoods

-K Number of ancestral populations

Optional:

-fname Ancestral population frequencies

-qname Admixture proportions

-outfiles Prefix for output files

-printInfo print ID and mean maximum allele frequency (maf) for the SNPs that were analysed

Setup:

-seed Seed for initial guess in EM algorithm (a number lower than 1M is preferred).

The same seed can be used to reproduce the analysis, and 3 different seeds can be used to test convergence.

-P Number of threads

-method 0 indicates no acceleration of EM algorithm. Please refer to the paper for more information.

-misTol Tolerance for considering a site as missing. Default = 0.05.

To include high quality genotypes only, increase this value (for example, 0.9)

Stop criteria:

-tolLike50 Loglikelihood difference in 50 iterations. Default= 0.1

-tol Tolerance for convergence. Default = 1x10^-5. Use maller values for higher accuracy.

It's the maximum squared difference of F and Q (please refer to the paper for formula).

-dymBound Use dymamic boundaries (1: yes (default) 0: no).

-maxiter Maximum number of EM iterations. Default = 2000 (high value).

In case it doesn't converge, this value needs to be higher.

Filtering:

-minMaf Minimum minor allele frequency. Default = 5%

-minLrt Minimum likelihood ratio value for maf>0. Default = 0

-minInd Minumum number of informative individuals. Default = 0

It only keeps sites where there is at least x # of individuals with NGS data.

Input File

The input file contains genotype likelihoods in a .beagle file format [5]. and can be compressed with gzip.

BAM files

If you have BAM files you can use ANGSD to produce genotype likelihoods in .beagle format. Please see Creation of Beagle files with ANGSD

VCF files

If you already have made a VCF file that contains genotype likehood information then it should be possible to convert .vcf files with genotype likelihoods to .beagle file via vcftools [6]

vcftools --vcf input.vcf --out test --BEAGLE-GL --chr 1,2

Chromosome has to be specified.

You can also use bcftools' [7] 'query' option for generating a .beagle file from a .vcf file.

Output Files

The analysis performed by NGSadmix produces 4 files:

• Log likelihood of the estimates: a .log file that summarizes the run. The Command line used for running the program, what the likelihood is every 50 iterations, and finally how long it took to do the run.

• Estimated allele frequency: a zipped .fopt file, that contains an estimate of the allele frequency in each of the 3 assumed ancestral populations. There is a line for each locus.

• Estimated admixture proportions: a .qopt file, that contains an estimate of the individual's ancestry proportion (admixture) from each of the three assumed ancestral populations for all individuals. There is a line for each individual.

Run command example

Download the input file

wget popgen.dk/software/download/NGSadmix/data/input.gz

Execute NGSadmix

./NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05

Input file = input.gz

Ancestral Populations K=3

Computer cores = 4 (-P 4).

Output prefix = myoutfiles (-o myoutfiles)

SNPs with MAF > 5% (-minMaf 0.05)

Detailed Examples and Tutorial

Please refer to the tutorial's page [8]

Citation

http://www.genetics.org/content/early/2013/09/03/genetics.113.154138.full.pdf

Skotte, L., Korneliussen, T. S., & Albrechtsen, A. (2013). Estimating individual admixture proportions from next generation sequencing data. Genetics, 195(3), 693–702. doi:10.1534/genetics.113.154138

Bibtex

% 24026093

@Article{pmid24026093,

Author="Skotte, L. and Korneliussen, T. S. and Albrechtsen, A. ",

Title="{{E}stimating {I}ndividual {A}dmixture {P}roportions from {N}ext {G}eneration {S}equencing {D}ata}",

Journal="Genetics",

Year="2013",

Pages=" ",

Month="Sep"

}