Run Marker Dependency Filtering (MDF) locally

1. Download the MDF script and corresponding bash file. Only the file names in the bash script need to be modified. The script must be run on a Linux distribution. Sample association, mapping, and marker dependency files can be downloaded from the sample files page.
2. Change the path of the MARFILE="../resources/gwas/CAD2.new.txt" to the path of the association (e.g. GWAS) file, a two column ('MARKER', 'VALUE') tab delimited file with biological markers (e.g. SNPs) in the 'MARKER' column and association strength (e.g. -log10 transformed p-values) in the 'VALUE' column.
3. Change the path of the GENFILE="../resources/mapping/gene2loci.020kb.txt" to the pathway to the mapping file, a two column ('GENE', 'MARKER') tab delimited file with biological markers (e.g. SNPs) in the 'MARKER' column and corresponding genes in the 'GENE' column.
4. Change the path of the MDSFILE="../resources/linkage/ld70.ceu.txt" to the pathway to the dependency file, a three column ('MARKERa', 'MARKERb', WEIGHT) tab delimited file that defines the dependency structure (e.g. linkage disequilibrium) between markers.
5. Optionally, the output path for the dependency corrected association and mapping files can be specified, OUTPATH="output/", and the percentage of top associated markers can be limited to speed computation, NTOP=0.5. The output, dependency corrected association and mapping files, can then be used in the MSEA pipeline.