Recently, there have been a few threads on creating tag synonyms. I think most of these are not really synonyms. The following shows my thoughts about what are synonyms and what are not. I will also talk about meta-tags, as it is related and has been mentioned a few times.
To begin with, I need to point out that concepts are often organized into a certain hierarchy. For example,
alignment => nucleotide-alignment => read-alignment. This is related to the discussion below. I would also encourage people to have a look at the tag synonym page at SO. I don't think they are all perfect, but they are very informative.
In the SO tag synonym page, there are real synonyms like "format" vs "formats", "swift-3" vs "swift3" or "amazon-rds" vs "aws-rds". In these examples, the two tags are interchangeable. The relationship is obvious most of time.
What is harder to tell is semi-synonym: "swift3" vs "swift3.1" or "bash" vs "bash-function". For such pairs, one of the tag is conceptually the parent of the other tag. We create such synonyms when the child tag is unnecessarily narrow. Judging "unnecessity" is subjective. We have to take the habit of the community into account when making the decision.
Back to our recent examples:
sam vs bam. I think they are different enough and are not synonyms. "sam" is also conceptually the parent of "cram", "cSRA", "biohdf" and other binary representations of sam. If most of us still prefer to merge them, I would take "sam" as the master tag.
mapping vs read-mapping. As most others said, they are not because many "mapping" related problems have nothing to do with "read-mapping". Similarly, "read-mapping" is only one type of "alignment". They are not synonyms.
Now meta-tags. I think we might be sometimes confusing a meta-tag with a general tag. For example, "alignment" is a general tag, but it still sufficiently narrows the question down to a specific field. In contrast, the examples on the meta-tag page (e.g. "beginner" and "best-practice") are applicable to almost any fields. Here are some recent discussions related to meta tags:
format vs file-format. I think the latter is a synonym of the former. In addition to files, I am not sure what other formats we talk about daily. I am also ok to separate them out if others can prove me wrong, but "format" is definitely not a meta tag. A lot of existing questions are unrelated to format.
alignment vs sequence-alignment. Again, I think the latter is a synonym of the former because in bioinformatics, alignment is almost always applied to sequences or data structures derived from sequences (e.g. profiles, secondary structures or graphs). Alignment has a lot of applications, but it is only a small field in bioinformatics. "alignment" is not a meta-tag, either.