This scenario configures Varlociraptor to perform tumor/normal calling. Contamination of the tumor sample by normal cells is specified. Varlociraptor is able to use the known contamination with normal cells to also infer information about potential germline variants. Of course, distinguishing between germline and somatic mutations in the tumor/relapse is never certain in such a scenario, but the probabilities are accurately split between the two. 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
genome-size: 3.5e9
samples:
normal:
sex: male
tumor:
sex: male
somatic-effective-mutation-rate: 1e-6
inheritance:
clonal:
from: normal
somatic: true
contamination:
by: normal
fraction: 0.1
relapse:
sex: male
universe: "[0.0,1.0]"
contamination:
by: normal
fraction: 0.2
events:
somatic_tumor: "tumor:]0.0,1.0]"
somatic_relapse: "tumor:0.0 & relapse:]0.0,1.0]"
germline: "normal:0.5 | normal:1.0"