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).
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
This script (and
Makefile):
/usr/local/packages6/apps/intel/15/AdmixTools/4.1)libifcore rather than gfortran and uses MKL for BLAS and LAPACK functions)this module file as /usr/local/modulefiles/apps/intel/15/AdmixTools/4.1