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

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[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 = 60
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 = 10
clonal_threshold = 0.3
absent_threshold = 0.0
mapq = 0
base_phred_quality = 0
min_components = 2
max_components = 3
indel = True
indel_flank = 100

[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 = 0.3
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 = 10
mapq = 0
base_phred_quality = 0
indel = True