Index assignment issues in families with n>=4 members

[Nicolai-vKuegelgen]

Describe the bug In each case/family one individual is set as the index and in families with n>3 members, this is a potentially non-trivial issue. Specifically for Inheritance Variant filters the correct assignment (shown as 'Trio role') is critical so that filters will work correctly.

In the particular case observed (n=4, 2 parents, 2 children, only one affected) there is a clearly intended index case (only affected family member, Family name == (Index) individual name), however the wrong (first) family member is assigned as Index in Varfish.

To Reproduce Steps to reproduce the behavior:

1. Have a family with n>=4 members, incl 2 parents and a 2 siblings, only 1 affected
2. Error likely only happens if the intended index (affected) is not the first of the sample of the family
3. In the details for Inheritance-Filters the wrong sample is marked as index (in the 'Trio Role' column)

See also screenshot.

Expected behavior Index assignment should either:

• take at least Affected status, and optionally Family-Individual-Names into account (on top of Sample relationships)
• or be user editable (i.e. manually assigning the index to role to a specific sample, this would also allow solve ambiguous cases with two affected siblings)

Screenshots

[stolpeo]

RCA

The wrong index patient was assigned. This happened due to a bug / missing feature in VarFish CLI.

https://github.com/varfish-org/varfish-cli/issues/133

It needs to be evaluated if there is still a problem after assigning the correct index patient.

[stolpeo]

We should allow changing the index patient in the case overview. We already allow changing the pedigree. However, both actions can falsify existing queries. They should be removed once a change happens.