mutation_blacklist_file	none
skip_permutations	true
build	hg38
exclude_noncoding	1
enforce_target_list	1
mutation_type_dictionary_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/mutation_type_dictionary.v5.txt
coverage_models_mat_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/hg38/coverage_models.agilent.mat
target_list_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/hg38/target_list.gencode25.txt
context_and_effect_fwb_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/hg38/context_and_effect_track.fwb
context_and_effect_categs_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/context_and_effect_dict.txt
covariates_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/hg38/covariates.agilent.txt
basewise_coverage_fwb_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/coverage_basewise.fwb
conservation_fwb_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/conservation46.fwb
FixedWidthBinary_jar_file	/cromwell_root/getzlab-workflows-reference_files-oa/MutSig2CV/FixedWidthBinary.jar