@@ -11,13 +11,16 @@ The current pipeline integrate the following workflow:
The following Item are necessary to run JASS pipeline
1. --input_folder : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv)
1. --meta_data : A path toward a meta-data file describing GWAS (see example file in ./input_files/test1.csv)
2. --gwas_folder : A path toward a folder containing the summary statistics to analyze
3. A folder containing a Reference Panel in the .bim, .bed, .fam format
4. If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line
3. --ref_panel :A folder containing a Reference Panel in the .bim, .bed, .fam format
4. --ld-folder : A path toward a folder containing LD matrices (that can be generated from the reference panel with the raiss package as described here : http://statistical-genetics.pages.pasteur.fr/raiss/#precomputation-of-ld-correlation)
5. --group If you wish to compute joint analyses with the pipeline, a group file with the each phenotype group written on a separated line
## Optional parameters
. A path toward a folder to write pipeline results (inittable, worktable...). by default results will be publish in the workflow directory.
* --output_folder : A path toward a folder to write pipeline results (inittable, worktable...). by default results will be publish in the workflow directory.