configuration_cna

spaceranger_dir : <Replace with Spaceranger directory>
snp_dir : <Replace with output directory of preprocessing>
output_dir : <Replace with output directory, must be existing>

# supporting files and preprocessing arguments
geneticmap_file : <Replace with CalicoST directory>/GRCh38_resources/genetic_map_GRCh38_merged.tab.gz
hgtable_file : <Replace with CalicoST directory>/GRCh38_resources/hgTables_hg38_gencode.txt
normalidx_file : None
tumorprop_file : None
supervision_clone_file : None
filtergenelist_file : <Replace with CalicoST directory>/GRCh38_resources/ig_gene_list.txt
filterregion_file : <Replace with CalicoST directory>/GRCh38_resources/HLA_regions.bed
secondary_min_umi : 300
bafonly : False

# phase switch probability
nu : 1.0
logphase_shift : -2.0
npart_phasing : 3

# HMRF configurations
n_clones : 3
n_clones_rdr : 2
min_spots_per_clone : 100
min_avgumi_per_clone : 10
maxspots_pooling : 7
tumorprop_threshold : 0.5
max_iter_outer : 20
nodepotential : weighted_sum
initialization_method : rectangle
num_hmrf_initialization_start : 0
num_hmrf_initialization_end : 1
spatial_weight : 1.0
construct_adjacency_method : hexagon
construct_adjacency_w : 1.0

# HMM configurations
n_states : 7
params : smp
t : 1-1e-5
t_phaseing : 0.9999
fix_NB_dispersion : False
shared_NB_dispersion : True
fix_BB_dispersion : False
shared_BB_dispersion : True
max_iter : 30
tol : 0.0001
gmm_random_state : 0
np_threshold : 1.0
np_eventminlen : 10

# integer copy number
nonbalance_bafdist : 1.0
nondiploid_rdrdist : 10.0