Note: This workflow has now been superceded by eQTL-Catalogue/colocalisation.

colocWrapper

Simple workflow to perform colocalisation analysis between GWAS summary statistics from the GWASCatalog and eQTL summary statistics from the eQTL Catalogue.

Example

Load dependencies

module load nextflow
module load singularity

For GWAS Catalog summary statistics, please use:

nextflow run main.nf\
 --gwasFile testdata/gwas_file.tsv\
 --studyFile testdata/study_file.tsv\
 --gwas_type 'GWASCatalog'\
 -profile coloc\

For internal summary statistics, please use:

nextflow run main.nf\
 --gwasFile testdata/gwas_file_Alasoo_2018.tsv\
 --studyFile testdata/study_file.tsv\
 --gwas_type 'Alasoo_2018'\
 -profile coloc

Depedencies

The Docker container with all of the required dependencies to run the colocalisation pipeline is available from here: https://hub.docker.com/r/kauralasoo/coloc-wrapper