SMuRF/config_15cov.ini at master · ToolsVanBox/SMuRF · GitHub

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
[SMuRF]
threads = 8
blacklist = /hpc/pmc_vanboxtel/resources/Mutation_blacklists/MSC_healthyBM_raw_variants_hg38.bed,/hpc/pmc_vanboxtel/resources/Mutation_blacklists/Fetal_15x_raw_variants_hg38.bed
qual = 100
mq = 55
sample_gq_homozygous = 10
sample_gq_heterozygous = 99
sample_gq_homref = 10
control_gq_homozygous = 10
control_gq_heterozygous = 99
control_gq_homref = 10
indel_gq_homozygous = 99
indel_gq_heterozygous = 99
indel_gq_homref = 20
coverage = 5
clonal_threshold = 0.15
absent_threshold = 0.0
mapq = 0
base_phred_quality = 0
min_components = 2
max_components = 3
indel = True
indel_flank = 100
known_variant_flag_ids = dbNSFP_ExAC_AF dbNSFP_1000Gp3_AF GoNLv5AF
know_variant_flag_values = 0.1 0.1 0.1

[Driver]
threads = 8
effect = MODERATE|HIGH
genes = /hpc/pmc_vanboxtel/resources/hotspot_genes/cosmic_cancer_gene_census_09052019.txt
qual = 60
mq = 30
clonal_threshold = 0.15
absent_threshold = 0.0
sample_gq_homozygous = 10
sample_gq_heterozygous = 20
sample_gq_homref = 20
control_gq_homozygous = 10
control_gq_heterozygous = 10
control_gq_homref = 20
indel_gq_homozygous = 60
indel_gq_heterozygous = 60
indel_gq_homref = 20
coverage = 5
mapq = 0
base_phred_quality = 0
indel = True