Phenotype penetrance probability file
Input file
Same format as the output file.
Output file
This .pheno_penetrance_prob.txt file contains phenotype penetrance probabilities
for each distinct genotype impacting a phenotype.
These probabilities encode the relationship between genotypes and phenotypes.
The file should include all phenotypes present in phenotype files
(current functionality works only with one locus and one trait).
There are four lines per locus,
containing conditional probabilities of
all phenotypes for a given phased genotype,
including phenotyping errors or other deviations.
Each column represents a different phenotype state
(ordered from 0 to the total number of states), and
each row represents the phased genotypes
(aa, aA, Aa, and AA).
That is, the values within a row
form a conditional probability distribution
of phenotypes for the corresponding phased genotype.
Example for a monogenic recessive binary trait with 10% phenotyping error:
0.9 0.1
0.9 0.1
0.9 0.1
0.1 0.9