WIFA-X	Identification of cancer-driver genes in focal genomic aberrations from whole exome sequencing data
	You can start WIFA-X analysis from your own log2 copy number input instead of using provided 'quantify_copy_number_aberration.r' code. If you want to use normalized log2 ratio signal from EXCAVATOR2 program, use 'copy_number_aberration_from_EXCAVATOR2.r' code. Shell>copy_number_aberration_from_EXCAVATOR2.r <SAMPLE FILE LIST> <DIR OUTPUT> <NUM PROCESSES> SAMPLE FILE LIST : The file path of the table containing unique sample identifiers and path of HSLMResults from EXCAVATOR2 program DIR OUTPUT : The path of output file directory NUM PROCESSES : The number of clusters to process concurrently Here's an example list of SAMPLE FILE LIST id path S003 /home/tom/ExperimentalFileAnalysis/Results/sample3/HSLMResults_sample3.txt S009 /home/tom/ExperimentalFileAnalysis/Results/sample9/HSLMResults_sample9.txt S015 /home/tom/ExperimentalFileAnalysis/Results/sample15/HSLMResults_sample15.txt S029 /home/tom/ExperimentalFileAnalysis/Results/sample20/HSLMResults_sample29.txt After generating log2 copy number file using 'copy_number_aberration_from_EXCAVATOR2.r', you can run the remaining steps from 'identify_focal_aberrations.r'. Please refer to the manual pdf file.