This scenario configures Varlociraptor to perform tumor/normal/relapse calling. The model is configured with prior assumptions about mutation rate and heterozygosity. Note that you should configure these with your own expetise or via literature research. The values shown here are only examples.
species:
heterozygosity: 0.001
germline-mutation-rate: 1e-3
ploidy:
male:
all: 2
X: 1
Y: 1
female:
all: 2
X: 2
Y: 0
samples:
tumor:
sex: male
somatic-effective-mutation-rate: 1e-6
inheritance:
clonal:
from: normal
somatic: false
contamination:
by: normal
fraction: 0.15
relapse:
sex: male
somatic-effective-mutation-rate: 1e-6
inheritance:
subclonal:
from: tumor
contamination:
by: normal
fraction: 0.1
normal:
somatic-effective-mutation-rate: 1e-10
sex: male
events:
somatic_tumor: "normal:0.0 & tumor:]0.0,1.0]"
somatic_relapse: "normal:0.0 & tumor:0.0 & relapse:]0.0,1.0]"
germline: "normal:0.5 | normal:1.0"
somatic_normal: "normal:]0.0,0.5["