parameters.yaml

---
# set random seed
random_seed: 123
tree_seed: 123


# signature parameters
list_of_bases: ['A', 'C', 'T', 'G']
list_of_pairs: ['CA', 'CG', 'CT', 'TA', 'TC', 'TG']
sig_file: './data/signatures.txt'
num_signatures: 78
use_signatures: False
signature_alpha: 10

#genome and exome delimiters
full_genome: './data/hg38.fa'
EXON_FILE: './data/exonsegments.txt'

#parameters for the full simulation. The program will sample randomly from each list
num_samples_list: [7]
num_tumors_list: [2]
# frag length should be at least 100, and the read length should be less than the frag length
read_len_list: [75, 150, 500, 2000]
frag_len_list: [150,200, 1000, 3000]

#concentration of the clones
alpha_list: [10]

#can be True or False for these
paired_list: [True]
WES_list: [False, True]

use_leaf_only: False
error_rate_list: [0.0, 0.0, 0.0, 0.00001,0.00001,0.0001, 0.001]
clone_list: [5]

#rate list define the tumor mutations, can define or change however you want. 
ultralow_rates_list: &ultralow_rates_list [1.e-15]
low_rates_list: &low_rates_list [1.e-15, 1.e-13, 1.e-10]
medium_rates_list: &medium_rates_list [5.e-9, 4.e-10, 9.e-10, 3.e-9]
high_rates_list: &high_rates_list [3.e-8, 9.e-9, 7.e-9]
ultrahigh_rates_list: &ultrahigh_rates_list [5.e-8,5.e-7,6.e-7,5.e-8,1.e-7]
coverage_list: [2, 5, 10, 15,15, 25,25, 30,30]
pop_list: [8.e+8] #recommend to keep close to this value
num_single_cell_list: [0]
liquid_biopsy_list: [False]
batch_size: 1
subblock_size: 1
LSH_hash: False #If false, doesn't explore alternate reads for WES and uses breakpoints in EXON_FILE
LSHStringNum: 10000000 #G_N in the paper -- the sampling number
kmer_len: 50
num_perm: 64
thresh: 0.33
ctdna_frac_list: [0.96] #fraction of real tumor reads in liquid biopsy

#reference/normal sequencing parameters
ref_coverage: 30 #random.choice(coverage_list)
ref_clones: 5  # this doesnt matter
ref_paired: True
ref_WES: False
ref_erate: 0.0 #random.choice(error_rate_list)

#SNV, CNV, DEL, DELSMALL, INVERSION, TRANSLOCATION, BFB, CHROMOTHRIP, CHROMOPLEX, INSERTIONSMALL, KATAEGIS, ANEUPLOIDY
list_of_rates: [*high_rates_list, *ultralow_rates_list, *high_rates_list, *ultralow_rates_list, *high_rates_list, *ultralow_rates_list, *ultralow_rates_list, *ultralow_rates_list, *ultralow_rates_list, *ultralow_rates_list, *ultralow_rates_list, *ultralow_rates_list]