Pipeline-Tools

Pipeline-Tools is a collection of command line tool for manipulating and summarizing VCF files.

Installation

Stand-alone installation

Pipeline-Tools is currently designed only for Linux systems. You will need to install and configure the following tool:

1. Python v2.7.*

   You can check your Python version by running the following command in your terminal:

   $ python -V
   Python 2.7.10

   To install the correct version of Python, visit the official Python website.

2. Python packages: numpy, scipy, pandas, matplotlib, and pyVCF

   You will need pip to install the above packages. After installing pip, run the following commands in your terminal:

   # Upgrade pip
   sudo pip install -U pip
   
   pip install numpy
   pip install scipy
   pip install pandas
   pip install matplotlib
   pip install pyVCF

3. Clone the Pipeline-Tools repo

   # clone the repo
   git clone https://github.com/alexwaldrop/Pipeline-Tools.git

Docker Installation

Pipeline-Tools is maintained as a docker image and can be ported anywhere Docker is available.

The only pre-requisite here is the Docker client. Please execute the following command line to see if your system already have Docker-client installed or not.

$ sudo docker --version

If Docker is not installed on your system, you can get it from Docker-client.

After the Docker set up, please pull the Pipeline-Tools Docker image from the Docker Hub. To do so, please run the following command line:

$ sudo docker pull alexwaldrop/pipeline-tools:latest

You can run any of the Pipeline-Tools modules as Docker containers as follows:

$ sudo docker run --rm --user root alexwaldrop/pipeline-tools:latest "RecodeVCF.py --help"
$ sudo docker run --rm --user root alexwaldrop/pipeline-tools:latest "CatRecodedVCF.py --help"
$ sudo docker run --rm --user root alexwaldrop/pipeline-tools:latest "SummarizeVCF.py --help"
$ sudo docker run --rm --user root alexwaldrop/pipeline-tools:latest "CatVCFSummary.py --help"

Submodules

At present, Pipeline-Tools contains two tools for VCF processing:

RecodeVCF

Transforms VCF genotype calls, annotations into searchable/sortable RecodedVCF format. Complete Documentation found here.

SummarizeVCF

Summarizes variant features based on annotations contained in a VCF. Complete Documentation found here.

Project Status

Pipeline-Tools is actively under development. To request features, please contact the author listed below.

Authors

• Alex Waldrop