NGSremix

NGSremix is a software tool for estimating relatedness coefficients from admixed populations with low depth sequencing data. When working with low depth sequencing data it takes as input genotype likelihoods in beagle format. NGSremix also integrates relateAdmix, the predecessor to estimate relatedness form admixed populations, that assumed genotypes are known or are accuratelly called. When you have called genotypes you can use them as input in binary plink format.

NGSremix uses known admixture proportions and populaiton allele frequencies to account for the confounding effects of admixture in relatedness inference. To do so it also requires as input a file with admixture proportions (Q) and a file with ancestral population allele frequencies (F). With low depth data Q and F can be estiamted with NGSadmix that takes also as input genotype likelihoods in beagle format. When having called genotypes, Q and F can be estimated with ADMIXTURE (it would work with the esitamtes from other software such as STRUCTURE). Importantly, the admixture proporitons need to be accurate and reflect actual population structure, otherwise relatedness estimates might not be accurate.

Install

First clone the code

git clone https://github.com/KHanghoj/NGSremix.git

go to the scr folder that contains the C++ files and type

cd NGSremix/src
make -f CPP_Makefile

Arguments

To get the arguments available for NGSremix type the following:

./NGSremix

Arguments:
	-beagle    [str] name of the gzipped beagle file (for running from genotype likelihoods)
	-plink     [str] prefix of the binary plink file (excluding the .bed; alternative to -beagle for running from called genotypes))
	-fname     [str] path to ancestral population frequencies file (ending in .fopt.gz if estimated with NGSadmix, .P if estimated with ADMIXUTRE)
	-qname     [str] path to admixture proportions file (ending in .qopt if estimated with NGSadmix NGSadmix, .Q if estimated with ADMIXTURE)
	-o         [str] name of the output file

Paired and Parental Ancestry Estimation
	-bothanc 1 [int] Estimates paired and parental ancestries for each individual. Note Relatedness will NOT be estimated. [Default -bothanc 0]

Setup:
	-P         [int] Number of threads
	-seed      [uint]
	-tol       [float] Lower tolerance for excluding admixture/paired ancestry estimates [Default: 0.001]
	-select    [Comma separated (1,2,3) and/or range with dash (1-3), 1-based indexes] Individuals to do estimates for
	-notcool 1 [int] Disables paired ancestry. [Default -notcool 0] 
Legacy:
	-F 1       if you want to estimate inbreeding
	-autosomeMax 22	 autosome ends with this chromsome

Examples

We include two small datasets as test examples to run the method.

Genotype likelihoods

The example for genotype likelihoods has 6 individuals and 10000 sites. The example is a subset of individuals shown in figure 3 of the NGSremix paper.

The ancestry proportions and allele frequencies are already estimated with NGSadmix using 3 source populations with a larger dataset that includes unrelated individuals. The dataset is not included here, but we assume it is called beagle.gz and include the NGSadmix commnad for guidance:

NGSadmix -likes beagle.gz -K 3 -outfiles 3

This will generate a file with admixture proporitons Q called 3.qopt and a file with population allele frequencies F called 3.fopt.gz. The script subsample.py was used to keep only 6 related indivdiuals and subsample to 10000 sites. We can then use NGSremix to estiamte relatedness:

../src/NGSremix -beagle test.beagle.gz -qname test.3.qopt -fname test.3.fopt.gz -seed 1 -o res -P 1

Called genotypes

The example for called genotypes consists of 50 individuals that are admixed from 2 source populations.

The example requires that ADMIXTURE software and NGSremix are installed

cd data

# First run Admixture using a plink ".bed" as input to produce population specific allele 
# frequencies (smallPlink.2.P)  and individual ancestry proportions (smallPlink.2.Q).
# (note other programs can be used instead of Admixture, e.g. Structure and FRAPPE)
admixture smallPlink.bed 2 

# Then run NGSremix with plink bed, bim and fam files plus the Admixture output files as input
../src/NGSremix -plink smallPlink -f smallPlink.2.P -q smallPlink.2.Q -P 20