mrcieu/haprap repository overview

HAPlotype Regional Association Program (HAPRAP)⁠ is a fine mapping method which uses GWAS summary statistics and haplotypes from an individual-level reference panel. This image is set up to provide a consistent environment for HAPRAP as it depends on older versions of numpy and scipy, which may not be in use in your working environment.

⁠Use

To start an interactive session in a Docker container please run:

docker run -it mrcieu/haprap bash

Once you see the container bash prompt you can run HAPRAP. To run the example analysis use:

python HAPRAP.py --hap input_example_APOE/APOE_LDL_1000G.phased.haps --summary input_example_APOE/APOE_LDL.ma --out test

⁠Further information

See HAPRAP website⁠ for further details

If you have found this resource useful, please cite the following work: Zheng J, et al HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics. Bioinformatics 2016, 33(1):79-86⁠

We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to [email protected]⁠