ConvPhase

A convenient phase program.

The purpose of this program is to combine PHASE and SeqPHASE into a single python package, while making some crucial configuration options available.

Unfortunately, internal communication between PHASE and SeqPHASE is done through Fasta files. However, an iterative protocol was implemented to parse and write common Python datatypes. It is also possible to work with TSV and Fasta variants (MolD, HapView) by leveraging Taxi2.

This is a computational backend. For the GUI application, please visit ConvPhaseGui.

Installation

ConvPhase is available on PyPI. You can install it through pip:

pip install itaxotools-convphase

Executables

Download and run the standalone executables without installing Python from the latest ConvPhaseGui release page.

No executables are currently provided for the command-line tool.

Usage

The package comes with a command-line tool:

convphase examples/simple.fas ambiguous.fas
convphase examples/simple.tsv phased.tsv -p 0.4 -q 0.4

The program will replicate the input file format for the output file.
Allele identifiers are appended to the individual identifiers.

The following options from PHASE are available:

• phase threshold (-p)
• allele threshold (-q)
• number of iterations (-n)
• thinning interval (-t)
• burn-in (-b)

For some examples on how to use the Python API, please have look at the scripts folder.

Dependencies

Building from source requires:

• C++ compiler (GCC, msvc)
• haxe & hxcpp

PHASE and SeqPHASE are included as git submodules.
Taxi2 is included as a setuptools dependency.

Citations

Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978--989.

Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73:1162-1169.

Flot, J.F. (2010) seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments. Mol. Ecol. Resour., 10, 162–166.