forked from raphael-group/CalicoST
-
Notifications
You must be signed in to change notification settings - Fork 0
/
configuration_cna_multi
57 lines (50 loc) · 1.52 KB
/
configuration_cna_multi
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
input_filelist: <Replace with the table file for multiple SRT slices>
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
alignment_files :
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