GASPeR: Genome wide Association Studie and Polygenic Risk analysis pipeline software with cluster support
Nextflow pipeline for full GWAS quality control, imputation, association analysis and polygenic risk score model creation&visualisation
To perform full analysis, follow environment preparation steps and simply type in the following command line:
$ nextflow pipeline.nf --input plink
where plink is a prefix of .bim .bed .map files.
One of the outputs, namely, manhattan plot of association summary statistics. Circle size signifies odds ratio.
Parameters as well as scripts supporting pipeline were selected according to Coleman et al. (2016) and supporting repository gwas_scripts by Joni Coleman. Imputation part of main pipeline contains significant code snippets from InSilicoDB by GenePlaza.