I've seen a lot of people on forums, Youtube and steam complaining that Dogmeat vanishes in Sanctuary, This is not the case.

There are 5-6 doghouses in Sanctuary where Dogmeat will hang out, If you simply wander around removing them with the scrap tool, You will clean up all the spots and eventually find him.

I spent hours online looking for a fix, But when i gave up and just started scrapping the place for parts, I found him chilling in a garden.

Hope this helps.