Collection of functions that can be used in silvar.
This is meant to be a collection of expressions that can be used in silvar expr.
Collection of expressions that can be used in slivar
Collection of functions that can be used in silvar.
This is meant to be a collection of expressions that can be used in silvar expr.
If parents are affected, it may not make sense to filter for homozygous recessive for example
In order to deal with multiple values in an INFO field, we need to parse by &
and find min/max where appropriate.
We should only call de-novo mutations if mom and dad are present. If not, it is not clear.
Add autosomal dominant MOI logic
We can consolidate many of the CSQ filters by making them a bit more generic
Because slivar computes compound-hets separately, we have to allow parents to be homozygous REF, if not it will be too stringent.
We received feedback that we should not use the affection status in the ped file to filter. Instead allow the user to determine which segregation rules to apply.
This makes sense for most, except AD. For AD we have to know which parent is affected, if not we are guessing. So will turn this off for all segregation rules except AD.
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