How to change the html of threaded comments? I want to display the comments on a node in a thread.

Not sure if I should use views or a template.
I want to change the html so that it matches boostrap markup
By using comment-wrapper.tpl I can change some of the html,
but I cant change the indent class.
Could you give a little more info on what you are trying to do?

If you want to add your view for displaying comments to a specific thread, please take a look at using panel from contrib (https://drupal.org/project/panels).

This module allows you to add views (and other components as well) to specific pages, other panels (when using mini panels) etc...