RelateAdmix

Brief description

This page contains information about the program called relateAdmix, which can be used to infer relatedness coefficients for pairs of individuals or inbreeding coefficients even if they are admixed. The program has both an R interface and a C interface. Below is a description of how to install and use each of them. To be able to infer the relatedness you will need to know the individuals admixture proportions and the allele frequencies in each of the possible populations. This can be done e.g. using the program ADMIXTURE as shown in the example of how to use the C interface.

Installation - Linux/MAC

Both the C and R versions of the program have been made for linux but should work on other unix like systems. You need to have zlib installed. Some MAC users might also have to use makevars

Windows is not supported

Download

I move all the code to github [1]

Installation of R package

If you have the devtools packages (https://github.com/hadley/devtools) installed in R then you can install the package i R directly from github

library(devtools)
install_github("aalbrechtsen/relateAdmix")

Or install from the command line

git clone https://github.com/aalbrechtsen/relateAdmix.git
R CMD INSTALL relateAdmix

or build and install

git clone https://github.com/aalbrechtsen/relateAdmix.git
R CMD build relate
R CMD INSTALL Relate_<add version number>.tar.gz

Problems with zlib

If your R installation for some reason does not link to your zlib (e.i. gzopen missing) or you have a really old zlib installation then you can install the R part using

rm relateAdmix/src/Cinterface.*
rm relateAdmix/src/Makefile #only needed if you compiled the C program
R CMD INSTALL relateAdmix

Installation of C/C++ program

git clone https://github.com/aalbrechtsen/relateAdmix.git
cd relateAdmix/src
cp CPP_Makefile Makefile
make

Run example

Run example using R

After installing the package you can load it into R and try the example

library(relateAdmix)
example(relate)

This shows an example of how to use the package. More information can be found in the man pages

?relate

Run example from terminal

After installing the C version of the program you can try running it on the example data set in the data folder, which consists of 104290 SNP for 126 individuals that are admixed from 2 source populations.

If you are in the src folder where you installed relateAdmix and you have the software ADMIXTURE installed this can be done as follows:

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

NB!. Only use binary plink (.bed) since ADMIXTURE switches allele frequencies when using .ped files

Quick R pdf plot from the commandline:

# Plot the results in R (R needs to be installed)
Rscript -e "r<-read.table('output.k',head=T,as.is=T);pdf('rel.pdf');plot(r[,4],r[,5],ylab='k2',xlab='k1');dev.off()"

Options

see options by running with out additional arguments:

../src/relateAdmix 
Arguments:
	-plink name of the binary plink file (excluding the .bed)
	-fname Ancestral population frequencies
	-qname Admixture proportions
	-o name of the output file
Setup:
	-P Number of threads
	-F 1	 if you want to estimate inbreeding

-plink [FILE]

The binary plink file without postfix

-f/-fname [FILE]

Ancestral population frequencies (e.g. estimated from ADMIXTURE with the .P filename

-q/-qname [FILE]

Ancestral admxiture proportions (e.g. estimated from ADMIXTURE with the .Q filename

-o [NAME]

Output filename

-P [INTEGER]

Number of threads (not implemented for inbreeding)

-F [0 or 1]

Use -F 1 if you want to estimate the inbreeding coefficient instead of relatedness

Output file format

Example of output

ind1    ind2    k0      k1      k2      nIter
0       1       0.999941        0.000038        0.000021        26
0       2       0.999979        0.000010        0.000011        29
0       3       0.999953        0.000029        0.000018        26
0       4       0.999952        0.000023        0.000025        26
0       5       0.999972        0.000020        0.000007        26
0       6       0.999995        0.000003        0.000002        26
0       7       0.999995        0.000003        0.000002        26
0       8       0.999894        0.000069        0.000038        32
0       9       0.999894        0.000069        0.000038        32
0       10      0.999903        0.000071        0.000026        26
0       11      0.999903        0.000071        0.000026        26

The first two columns are the individuals number. The next three columns are the estimated relatedness coefficients and the last column is the number of iterations used.

Input file format

The input consists of three files describignt the genotype data, a file with admixture proportions for each individual and a file with allele frequencies for each SNP for each source population. The genotype data files are plink bed/bim/fam files. And the remaining two files are in the output format for the program ADMIXTURE:

Example of the content of an admixture proportion file (for 3 populations)

0.531631 0.468359 0.000010
0.564461 0.435529 0.000010
0.850660 0.149330 0.000010
0.630527 0.369463 0.000010
0.747429 0.219346 0.033225
0.999980 0.000010 0.000010
0.999980 0.000010 0.000010
0.682072 0.317918 0.000010
0.000010 0.999980 0.000010
0.793133 0.206857 0.000010

Each row is an individual and each column is a population. The admixture proportions for each individual must sum to 1

Example of the allele frequency file (for 3 populations)

0.312722 0.208605 0.999990
0.881352 0.999990 0.966966
0.708206 0.838869 0.932119
0.427789 0.620694 0.532966
0.411998 0.622253 0.534072
0.427789 0.620694 0.532966
0.440817 0.581630 0.618751
0.733733 0.985281 0.953523
0.724083 0.451452 0.784607
0.811161 0.578612 0.787782

Each row is an SNP and each column is a population. When using plink files the allele frequency is the MAJOR allele frequency.

Citing and references

relateAdmix

Moltke, I, Albrechtsen, A (2013). RelateAdmix: a software tool for estimating relatedness between admixed individuals. Bioinformatics. pubmed bibtex

Inbreeding

The model used for inbreeding is described in Ida Moltke, Matteo Fumagalli, Thorfinn S Korneliussen, Jacob E Crawford, Peter Bjerregaard, Marit E Jørgensen, Niels Grarup, Hans Christian Gulløv, Allan Linneberg, Oluf Pedersen, Torben Hansen, Rasmus Nielsen, Anders Albrechtsen Uncovering the genetic history of the present-day Greenlandic population. Am. J. Hum. Genet.: 2015, 96(1);54-69 Article

ADMIXTURE

D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.

change log

• 0.14 made more MAC usable (I think). Thanks to Paul Lott for reporting it and for suggestions and Thorfinn Sand for changing it
• 0.13 added extra check for file exists to give instant errors + changes all printf to fprintf(stderr,
• 0.11 changed threading to a fixed pool of threads
• 0.10 optimized code
• 0.09 added error for when the number of sites and individuals does not match between files
• 0.08 fixed a bug that would sometimes print an extra line when multiple threaded
• 0.07 fixed a small leak