We handle the simpler case of a Trio with an affected child (ie proband/mother/father).
Variants are assigned to the following bins
F1ALT: Paternally inherited, in phase with affected child, ALT variant. F1REF: Paternally inherited, in phase with affected child, REF variant. F2ALT: Paternally inherited, out of phase with affected child, ALT variant. F2REF: Paternally inherited, out of phase with affected child, REF variant.
And vice versa for the mother. The only variants that fall into each of these situations are:
|Child GT||Father GT||Mother GT||Bin|
Menu: [analysis] -> [karyomapping]
Enter a gene name and click [Karyomap Gene] button.
A genome wide karyomap count is performed when you create a trio. This is useful for finding sample mixups.
This is summarised as Proband phase: 50.74% mum / 49.26% dad. Mum: 54.96%. Dad: 51.69%. and is visible on the gene analysis screenshot above and the Trio page.
Proband phase shows the child’s marker percentage from each parent. Mum%/Dad% = Percent of parent markers that are in phase in proband.
Here are some examples for various Trios:
|Description||PP mum||PP dad||Mum %||Dad %|
|Real Trio 1||53%||47%||52.1%||45.9|
|Real Trio 2||52.3%||47.7%||46.1%||45.9%|
|Bad Trio (Trio 1 with random dad)||60.2%||39.8%||52.1%||25.7%|
|Bad Trio (unrelated samples)||48.5%||51.6%||30.8%||29.8%|
|Bad Trio (mother/proband swapped)||60.8%||39.2%||86.9%||36.1%|
As a rough rule, you’d expect a minimum of 40% for an actual child.