lottpaul / selectiontools

Pipeline to take VCF through to Selection Analysis.

IMPORTANT

Crucial bug fixed in Fay and Wu's calculation.

If you have a old Forked version of selectionTools, you will need to update to the latest version on the master branch.

In your repo run the following command.

    git pull origin master 

Your version needs to be more recent that the commit dd6ceb045ea6f2a3f4ee2585416ea31cf2020049

selectionTools 1.0

Pipeline to take VCF through to Selection Analysis.

Software Prerequisites

The selection pipeline was developed on a 64-bit Ubuntu 13.04 system and has been tested on 64-bit Centos and Ubuntu 13.10 installations. The pipeline should work on any 64-bit linux system and OSX (without Fay and Wu's H).

• Python >= 2.6
• Bourne-again Shell (Bash)
• Perl >=5
• R >= 3.0.0
• GNU Autotools
• GCC
• Git
• Java >= 1.7 (for beagle)

Python Dependencies

• python-setuptools
• python-numpy
• python-scipy

If you are using python < 2.7 the python package argparse will need to be installed. Installation

After cloning or downloading and extracting running ./install.sh in the root directory will attempt to install the pipeline and all required dependencies.

By default the pipeline executables will be added to $HOME/.local/bin, you should add this directory to your executable path.

Config File

Each run of the pipeline requires the specification of settings in a config file. A default config file is generated after installation in the selectionTools directory named defaults.cfg. Detailed information on what the settings do and how to change them is avaliable in the pdf manual in the docs/ directory.

Single Population

To run the selection pipeline on a single population

selection_pipeline -c <chromosome number> -i <vcf input> --population <population name> \
--config-file <config_file> --cores <cpu cores>

To view the other options run the help.

selection_pipeline -h

Multiple Populations

To run the selection pipeline on multiple populations.

multipop_selection_pipeline -p <population file1> -p <population file2> \
-i <merged input vcf> --config-file <config file> 

For more information on population files consult the PDF manual specifically section 3.3.

To view the other options run the help.

multipop_selection_pipeline -h

Notes

With a Red Hat linux system you will need to extract the qctool scientific linux distribution located in the src directory.