Short description: AdmixInfer is designed to optimize the parameters of admixture model via maximum likelihood estimation and figure out the model best fit the data. The optimization is under assumption of HI (Hybrid Isolation), GA(Gradual Admixture), CGFR (Continuous Gene Flow Recipient) and CGFD (Continuous Gene Flow Donor) model.
AdmixInfer depend on boost library, make sure the boost is installed. Installation of boost can be found at http://www.boost.org/doc/libs/1_58_0/more/getting_started/unix-variants.html
It's very easy to compile from the source code by the following commands:
bash$ tar -zvxf AdmixInfer.tar.gz
bash$ cd AdmixInfer/src
bash$ make
After compiling, you will get the executable AdmixInfer, just typing the command below to get help information:
bash$ ./AdmixInfer -h or bash$ ./AdmixInfer --help
bash$ ./AdmixInfer --input ../example/sim1.seg
Example explanation: AdmixInfer will read the ancestral tracks from sim1.seg, after a while, the optimal model and corresponding generation will print to screen. The format will explained later
The following is output of the toy data:
//CMD: ./AdmixInfer -i example/sim1.seg
Reading ancestral tracks from example/sim1.seg
Start optimizing process...
Results summary
----------------------------------------------------------
Reference populations: 1, 2
Admixture proportions: 0.287948, 0.712052
Optimal-model: HI, generation: 51, likelihood: 50290.4
----------------------------------------------------------
The results show that the toy data. The simulated admixed population has two reference populations with label 1 and 2, corresponding mixture proportions are 0.287948 and 0.712052, the optimal model is HI, and the generation is 51. The simulated population is under HI model and 30% and 70% mixture proportions, admixture started 50 generations ago.
User can redirect the output to a file, such as:
bash$ ./AdmixInfer --input ../example/sim1.seg > sim1_opt.log
bash$ ./AdmixInfer -i ../example/sim1.seg -l 0.01 -u 0.5 -a 0.01 \
-b 100 -p 0.5 > sim1_fopt.log
Example explanation:
Again, AdmixInfer read ancestral tracks from file sim1.seg, discard the tracks shorter than 0.01 Morgan and longer than 0.5 Morgan, the significance level to compute confidence intervals is 0.01 (which will compute 99% confidence intervals), the number of bootstrapping is 100, and 50% tracks will sampled in each bootstrapping. Finally, the outputs will be redirected to sim1_fopt.log.
The results is:
//CMD: ./AdmixInfer -i example/sim1.seg -l 0.01 -u 0.5 -a 0.01 \
-b 100 -p 0.5
Reading ancestral tracks from example/sim1.seg
Start optimizing process...
Start bootstrapping process...
Bootstrap-1--> model: HI, generation: 51, likelihood: 19003.7
Bootstrap-2--> model: HI, generation: 51, likelihood: 18915.4
......
Bootstrap-100--> model: HI, generation: 51, likelihood: 18999.4
Finish bootstrapping, processing results...
Results summary
----------------------------------------------------------
Reference populations: 1, 2
Admixture proportions: 0.287948, 0.712052
Optimal-model: HI(100%)
Generation: 51.08, 99% confidence interval: (50.92, 51.24)
----------------------------------------------------------
Again, the optimal model we inferred is HI and generation estimated is 51.08 the 99% confidence intervals are (50.92, 51.24).
AdmixInfer is easy to use, only need one file, in which each line represents a ancestral track with the start point, end points, from which ancestry the track originates. The start and end points units are in Morgan.
For example:
0.00000000 0.34602058 Yoruba 0.34602058 0.34614778 French ...... 0.40759031 0.41517938 Yoruba
-i/--input <string>
This argument is required, in which user specify the filename of
input ancestral tracks, format described above.
-l/--lower [double]
This argument is optional, in which user specify the lower bound
to discard short tracks. The default is 0, which does not discard any
short tracks. However, due to method limitation in local ancestry
inference, very short tracks are generally not reliable.
-u/--upper [double]
This argument is optional, in which user specify the upper bound
to discard long tracks. The default is infinity, which does not discard
any long tracks.
-a/--alpha [double]
This argument is optional, in which user specify the significance
level to compute confidence intervals, this argument is used with
bootstrap. When the number of bootstrap is 1, AdmixInfer does not
compute confidence intervals. The default is 0.05, which will compute
the 95% confidence intervals.
-b/--bootstrap [integer]
This argument is optional, in which user specify the number of
bootstrapping repeats. The default is 1, which does not perform
bootstrapping.
-p/--proportion [double]
This argument is optional, in which user specify the proportion
of tracks in bootstrapping sampled. The default 1.0, which samples
equal size of tracks in each bootstrapping repeat.
-h/--help
Print help messages of all arguments and options
-q/--quiet
Running in quiet mode, default is off.
GNU GENERAL PUBLIC LICENSE Version 3
http://www.gnu.org/licenses/gpl-3.0.html
Questions and suggestions are welcomed, feel free to contact Shawn xyang619@gmail.com
When using AdmixInfer, please cite
Ni X, Yang X, Guo W, Yuan K, Zhou Y, Ma Z, Xu S. Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference. Sci Rep. 2016 Jan 28;6:20048. doi: 10.1038/srep20048. Erratum in: Sci Rep. 2016 May 23;6:26367. PMID: 26818889; PMCID: PMC4730239.