######cjm edits for TOBI####

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TOBI: Tumor Only Boosting Identification of Driver Mutations

Input: vcf files as described in "list file" from step0; maf file to generate "list file" #WXS bam files in `list_file`.

Ver. 1.2: Mar 22, 2016
cjmadubata modified from Alireza Roshan Ghias's code (Ver. 1.1: Nov 07, 2014 https://github.com/alireza202/TOBI.git TOBI)

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###varCall_filtering###
Step0. Run: varCall_filtering/maf_to_tobi_som_var_list.sh {path_to_maf} {output_true_somatic} 
	to generate list of  true somatic varints {output_true_somatic} 
	and list of case names patient.{output_true_somatic} (aka list_file)

Step1. Update tobi_config file for your samples, particularly location of list_file

VCF files are assumed to be in same folder with different sample names at beginning of file
followed by a common suffix
	e.g. path/to/vcf/files/TCGA-XX-XXXX-*suffix
	each TCGA-XX-XXXX represents one patient and one line in "list_file"

Step 2. Check the batch run file
	varCall_filtering/batch_multi_array.LGG_TCGA.sh_suffix 

Step 5. Run all samples using -AF flags:
	varCall_filtering/batch_multi_array.LGG_TCGA.sh_suffix --config /path/to/config_file 
	--steps AF --bam all -s 0 -e 0 --cluster hpc --filter on --vcfsuf oxoG.snp.capture.tcga.vcf
	# --bam -s -e flags are not used for VCF analysis

Step 6. Check number of lines in final file sizes, using the script below:
	varCall_filtering/tobi_out_empty.sh {main_outputdir_from_config} {list_file}	
	
If some cases did not run, find the problem, and run them again.

Step 7. Merge all final files for each case, and then all together using the script 
below:

	varCall_filtering/merge_all_tsvs.sh {list_file} {main_outputdir_from_config} {/path/to/output/table} {label_for_this_TOBI_run} 	

Step 7a. If using COSMIC after v66, need to replace "cnt" column with "cosmic_nsamp" for next TOBI steps
	sed -i '1s/cnt/cosmic_nsamp/' {/path/to/output/table}

### machine_learning ###
Step 8. Pre-processing using R. Needs customization each time.

	machine_learning/pre_processing.R