I’ve been trying to loosen the de novo caller criteria to include variants that are not present in the parents, but can be present in the child at an allele balance < 0.20. However, using the following command (or other iterations of it), it seems that the allele balance is somewhat clamped at 0.20.
de_novo_asc = hl.de_novo(mt, pedigree, pop_frequency_prior=mt.raw_AF_e, min_child_ab=0.000001, min_dp_ratio=0.00001, max_parent_ab = 0.001)
The distribution of the allele balances are as follows:
Is this the expected behavior? From previous studies we would expect more weight on variants between the 0.20 and 0+ range.