name=SherlockLung_LUAD_2025_DN2
input_dir=path/to/data/subclones_files/
output_dir=path/to/data/SherlockLung_LUAD_2025_DN2/
add_muts=TRUE
PLmethod=PlackettLuce
G=1
unobserved=notIncluded
driver_symbol_file=path/to/data/sherlock_driver_symbols.txt
nonsynonymous_mutation_file=path/to/data/sherlock_nonsyn_muts.txt
dpclust_data_dir=path/to/data/dp_data/
wgd_file=path/to/data/SherlockLung_WGDStatus.txt
sample_list=path/to/data/SherlockLung_AllHQ_LUAD_2025/SherlockLung_AllHQ_LUAD_2025_sample_group_2.txt
wcc_dir=path/to/data/WCC_bestClusterInfo/
assembly=hg38
chr_coords=path/to/Ordering_Model/reference_files/chromosome_coordinates_hg38.txt
centro_coords=path/to/Ordering_Model/reference_files/UCSC_GRC_combined_centromeres_hg38.txt
remove_acrocentric=TRUE
memory_saver=FALSE
bb_file_pattern=subclones.txt
estimate_MRCA=FALSE