ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

• convertf: See README.CONVERTF for documentation of programs for converting file formats.
• qp3Pop: See README.3PopTest for details of running f_3 test. This test can be used as a format test of admixture with 3 populations.
• qpBound: See README.3PopTest for details of running qpBound. This test can be used for estimating bounds on the admixture proportions, given 3 populations (2 reference and one target).
• qpDstat: See README.Dstatistics for details of running D-statistics. This is a formal test of admixture with 4 populations.
• qpF4Ratio: See README.F4RatioTest for details of running F4 ratio estimation. This program computes the admixture proportion by taking the ratio of two f4 tests.
• rolloff: See README.ROLLOFF/ README.ROLLOFF_OUTPUT for details for running rolloff. This program can be used for dating admixture events.

References:

• Paper

• AdmixTools website at Harvard.
• AdmixTools on Github.

• Module Name: AdmixTools (see the modules page for more information)
• Example files in /usr/local/apps/AdmixTools/examples/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load AdmixTools
[+] Loading AdmixTools 4.1 ...

[user@cn3144 examples]$ cp -r  $AMT_DATA/* .
[user@cn3144 examples]$ expfit.sh rolloff-test-parfile.par
Running rexpfit.r 
Input file:  ASW_CEU_YRI
Output file:  expfit_ASW_CEU_YRI
Expfit logfile: expfit_ASW_CEU_YRI.flog
Output plot: expfit_ASW_CEU_YRI.pdf
 expfit.sh rolloff-test-parfile.par
Jackknife logfile: expfit_ASW_CEU_YRI.log
  
Jackknife summary: ASW_CEU_YRI.jin
Jackknife mean:          5.468
Jackknife std. err:      0.253
[user@cn3145 test]$  expfit.sh rolloff-test-parfile.par
Running rexpfit.r 
Input file:  ASW_CEU_YRI
Output file:  expfit_ASW_CEU_YRI
Expfit logfile: expfit_ASW_CEU_YRI.flog
Output plot: expfit_ASW_CEU_YRI.pdf
Jackknife logfile: expfit_ASW_CEU_YRI.log

Jackknife summary: ASW_CEU_YRI.jin
Jackknife mean:          5.468
Jackknife std. err:      0.253

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. AdmixTools.sh). For example:

#!/bin/bash
# this file is called admix.sh

module load AdmixTools

convertf -p par.EIGENSTRAT.PED

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#] AdmixTools.sh

Create a swarmfile (e.g. AdmixTools.swarm). For example:

rolloff -p rolloff1.par > rolloff1.log 2>&1
rolloff -p rolloff2.par > rolloff2.log 2>&1
rolloff -p rolloff3.par > rolloff3.log 2>&1

Submit this job using the swarm command.

swarm -f AdmixTools.swarm [-g #] --module AdmixTools