@gregorgorjanc
According to the code's comment, there are many different parameters for peeling:
# Error terms:
# Peel down: Assume 0.00001 genotyping/mutation error for anterior terms.
# Peel up: assume 1% in genotypes when converting genotypes => probabilities
# Peel up: assume 1% error in segregation when converting called seg => probabilities.
# Peel up: assume 1% error when going from mate genotype probs => genotype probs.
# Peel up: 1e-8 error rate when marginalizing across mate genotypes (shouldn't need this with the mate genotype probs?)
# Peel up: additional 0.001 error rate when going from posterior -> genotype probabilities.
# Segregation: assumes 1% genotyping error when creating match between individual + parent
How to determine the values of these parameters needs to be investigated.
@gregorgorjanc
According to the code's comment, there are many different parameters for peeling:
How to determine the values of these parameters needs to be investigated.