UNDER ACTIVE DEVELOPMENT AND NOT READY FOR USE
pipeline_QTL¶
Python based pipeline for quantitative trait loci analysis.
For the general framework and workflow see project_quickstart docs and cgat-core.
Features¶
- Currently runs MatrixEQTL on an arbitrary number of inputs and outputs association files, basic plots such as qqplots.
Requirements¶
See requirements files and Dockerfile for full information. At the least you’ll need:
- cgat-core
- R >= 3.2
- Python >= 3.5
- r-matrixeqtl
- r-docopt
- r-data.table
- r-ggplot2
- stats_utils
Installation¶
pip install git+git://github.com/EpiCompBio/pipeline_QTL.git
To use¶
# Create a folder or a whole data science project, e.g. project_quickstart -n QTL_project
cd QTL_project/results
mkdir tests ; cd tests
# Copy or generate test files if needed. See scripts in this repository:
# https://github.com/EpiCompBio/pipeline_QTL/tree/master/tests
# Run as:
bash /path_to/create_QTL_infiles.sh /path_to_further_scripts/pipeline_QTL/tests
# You can also download test files from e.g.:
# wget -nH -np -r --cut-dirs=4 -A .txt http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/Sample_Data/
# https://github.com/gabraham/flashpca/tree/master/HapMap3 :
# wget https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_format/hapmap3_r2_b36_fwd.consensus.qc.poly.ped.bz2
# Once you have QC'd binary files in plink format and a molecular phenotype file with samples in columns and variables in rows, run:
pipeline_QTL --help
pipeline_QTL config
# Edit pipeline_QTL.ini to adjust the parameters you want, this is essential
pipeline_QTL show full -v 5
pipeline_QTL printconfig
pipeline_QTL plot full -v 5
pipeline_QTL make full --local -v 5
pipeline_QTL make make_report --local -v 5
open pipeline_report/_build/latex/pipeline_QTL.pdf
Bugs and Contributions¶
- Pull requests welcome!
- Please report bugs using the Issue Tracker
Thanks Mum and Dad