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AdmixTools

AdmixTools implements five genetics methods described for learning about population mixtures. Details of these methods/algorithms can be found in Patterson et al. (2012) Ancient Admixture in Human History (doi:10.1534/genetics.112.145037).

Usage

Load version 4.1 of AdmixTools with the command

module load apps/intel/15/AdmixTools/4.1

This module makes the following programs available (by adding their containing directory to the PATH environment variable); programs; these are documented in README files contained in the $ADMIXTOOLSDIR directory.

  • 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.

AdmixTools also comes with several examples. The example inputs and outputs can be found in $ADMIXTOOLSDIR/examples, whilst the example data the inputs reference are contained in $ADMIXTOOLSDIR/data

Installation Notes

Version 4.1

This script (and Makefile):

  1. Checks out a specific git commit of AdmixTools (def3c5d75d1b10fd3270631f5c64adbf3af04d4d; NB the repository does not contain any tags)
  2. Builds GNU Scientific library (GSL) v2.2 and installs into the AdmixTools final installation directory (/usr/local/packages6/apps/intel/15/AdmixTools/4.1)
  3. Builds AdmixTools (using v15.0.3 of the Intel Compiler and a customised Makefile (links against Intel libifcore rather than gfortran and uses MKL for BLAS and LAPACK functions)
  4. Installs AdmixTools in the aforementioned directory.
  5. Downloads the data needed to run the examples then runs the examples
  6. Installs this module file as /usr/local/modulefiles/apps/intel/15/AdmixTools/4.1