This scenario configures Varlociraptor to perform tumor/normal 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. In addition, contamination of the tumor sample by normal cells is specified.
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:
tumor:
sex: female
somatic-effective-mutation-rate: 1e-6
inheritance:
clonal:
from: normal
somatic: true
contamination:
by: normal
fraction: 0.1
normal:
sex: female
somatic-effective-mutation-rate: 1e-10
events:
somatic_tumor_high: "normal:0.0 & tumor:[0.1,1.0]"
somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
somatic_normal: "normal:]0.0,0.5["
germline: "normal:0.5 | normal:1.0"