Examples of "bad" plots

[hyanwong]

There are some cases where we think that tsqc indicates "bad stuff" (e.g. where there are long edges with no sites, etc). But a new user might not know what to look for. We should collect a gallery of these examples, with a bit of a discussion on each as to why we think this is a patter to be wary about. This could, I suppose, be in some sort of tutorial.

[barneyhill]

UKB 450K Exomes + Array (MAF>0.001). TTN (chr2) gene (tsinfer+tdate):

Overview

Mutations

Edges

Trees

Nodes

[barneyhill]

UKB 450K Exomes + Array (MAF>0.001). Entire chr21 (tsinfer+tdate):

Overview

Mutations


Edges

Trees

Nodes

Notes

Jerome recommended not to continue with this tree sequence due to these QC plots. Loading times for these plots are substantial (~mins per plot) but I think that's expected given the size of the ts.

[jeromekelleher]

Very interesting, thanks @barneyhill.

The TTN plots don't look terrible to me. I think it would be worth looking at the actual tree for a few random subsets (of say 10 samples) at a particular location, to get a feel for what the deep structure looks like.