This scenario configures Varlociraptor to perform a complex pedigree 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.
Note the reuse of the two denovo events in negated form as expressions in the other event.
Since the event space in Varlociraptor needs to cover all possibilites (absent event is always implicitly added), such statements can be very handy.
When performing such a negation, it is important to also include the absent event though (to avoid considering it twice).
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:
mother:
sex: female
father:
sex: male
child:
sex: male
inheritance:
mendelian:
from:
- mother
- father
sibling:
sex: female
inheritance:
mendelian:
from:
- mother
- father
events:
denovo_child: "(child:0.5 | child:1.0) & mother:0.0 & father:0.0"
denovo_sibling: "(sibling:0.5 | sibling:1.0) & mother:0.0 & father:0.0"
other: "!($denovo_child | $denovo_sibling | $absent)"