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raimondsre / GASPeR

Nextflow pipeline for full GWAS quality control, imputation, association analysis and PRS model creation&visualisation
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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.

Manhattan_plot

One of the outputs, namely, manhattan plot of association summary statistics. Circle size signifies odds ratio.

Acknowledgement

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.