Masked sites are still on json tree

Help and Getting Started
1

Hi! I try to mask three sites to avoid branch splitting due to it.
But I still see the branch with such mutations

That I have done:

Add to builds.yaml
files:
sites_to_mask: “defaults/sites_ignored_for_tree_topology.txt”
mask:
mask_sites: “sites numbers by space”

Add this sites to defaults/sites_ignored_for_tree_topology.txt file

Maybe it is important that two of these three mutations was in sites_ignored_for_tree_topology.txt previously by default

I will be glad to hear some reasons for existence of them on result tree. Thanks!

2

Hi Irena – those sites won’t have been used for the tree building, but we still infer those positions across the tree.

For instance, for our core builds we mask 21846 but you can still see the evolution of this base across the tree and thus know what nuc each sequence has at this position.