WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

Introduction

WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs

WASP is described in our paper: van de Geijn B*, McVicker G*, Gilad Y, Pritchard JK. "WASP: allele-specific software for robust discovery of molecular quantitative trait loci"

WASP has two parts, which can be used independently of each other:

1. Read filtering tools that correct for biases in allele-specific mapping.

2. A Combined Haplotype Test (CHT) that tests for genetic association with a molecular trait using counts of mapped and allele-specific reads.

The following directories and files are included with WASP. Each directory contains its own README file:

• CHT - Code for running the Combined Haplotype Test

• mapping - Mappability filtering pipeline for correcting allelic mapping biases

• snp2h5 - Contains snp2h5 and fasta2h5: programs for converting common SNP and sequence data formats (IMPUTE, VCF and FASTA) to an efficient binary format, HDF5.

• examples - Example data files that can be used to try out the Combined Haplotype Test.

• example_mapping_workflow.sh - A script illustrating how each step of the Mappability Filtering Pipeline can be run.

• example_cht_workflow.sh - A script illustrating how each step of the Combined Haplotype Test workflow can be run.

Dependencies

WASP is written in C and python and uses an efficient binary file format known as HDF5.

WASP depends on the following:

• python version 3.x

• numpy

• scipy.

• pysam version 0.8.4 or higher.

• the HDF5 C library version 1.8 or higher

• PyTables version 3.x

The easiest way to install HDF5, numpy, scipy and Pytables is to download and install Anaconda. Installing Anaconda is highly recommended. After installing Anaconda, configure [Bioconda] (https://bioconda.github.io/) and do conda install pysam, or download and install pysam directly.

Installation

1. Download and install Anaconda, (or download and install Numpy, Scipy, HDF5, and Pytables separately).

2. Configure Bioconda and install pysam:

   conda config --add channels r
   conda config --add channels bioconda
   conda install pysam

   Alternatively, download and install pysam yourself.

3. Make sure that the HDF5 library is in your library path. For example on Linux or OSX you can add the following to your .bashrc or .profile (replace $CONDA_PREFIX with your Anaconda installation directory if CONDA_PREFIX is not defined):

   export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH

4. Clone or download the WASP repository from github:

   # clone the WASP repository
   git clone https://github.com/bmvdgeijn/WASP.git
   
   # Alternatively download the respository instead:
   wget https://github.com/bmvdgeijn/WASP/archive/master.zip

5. Compile snp2h5 (optional: only needs to be done if you plan to use snp2h5 or fasta2h5). First modify the snp2h5/Makefile to point to the Anaconda (or HDF5) installation directory. For example open snp2h5/Makefile with a text editor and modify the HDF_INSTALL variable to point to your Anaconda installation directory:

   HDF_INSTALL = $(CONDA_PREFIX)

   Now compile snp2h5 using make:

   cd WASP/snp2h5
   make