I am using genome music path-scan to find signifiacntly mutated pathways.
genome music path-scan --gene-covg-dir gene_covgs --bam-list $bamList --pathway-file $pathwayKEGGFile --maf-file $maf --output-file $pathwayOutputFile -bmr 1.8E-6
The program requires KEGG pathway file. KEGG file used by music can be found here, https://raw.githubusercontent.com/ding-lab/parse-kegg/master/all_pathway_files/KEGG_052412 , but it is not updated from 2012. Can somebody share (if they have updated one) or help me to prepare this file in required format.