I'm afraid this is standard operating procedure on Stack Exchange sites. Comments are ephemeral, expressly designed to be deleted without warning. The idea is that comments should be used to ask for clarification, and then once consensus has been reached, they should be edited into the question or answer instead.
That's precisely what happened here. The claim that samtools mpileup is deprecated was incorrect, finswimmer meant that it was only deprecated when generating VCF files. Since finswimmer (not I) edited the answer to remove that claim, the comments were no longer relevant and since the entire comment thread was based on a misunderstanding, there was no reason to keep it around. It wasn't providing anything relevant to the actual question asked, so I deleted it. Here is a screenshot of the thread:
This is something that is often surprising for folks who come to SE from other online resources. But this really is how comments are supposed to work, and is explained in the relevant help page, parts of which I quote below::
Comments are temporary "Post-It" notes left on a question or answer. They can be upvoted (but not downvoted) and flagged, but do not generate reputation. There's no revision history, and when they are deleted they're gone for good.
When should I comment?
You should submit a comment if you want to:
- Request clarification from the author;
- Leave constructive criticism that guides the author in improving the post;
- Add relevant but minor or transient information to a post (e.g. a link to a related question, or an alert to the author that the
question has been updated).
When shouldn't I comment?
Comments are not recommended for any of the
- Secondary discussion or debating a controversial point; please use
So, as a general rule, if you want something to stay with a post, make it an edit and not a comment. This is a collaborative site, so editing to improve a post or add extra information is absolutely encouraged. Comments, however, are ephemeral.