Could you list some tools which take read-reference mapping as input?

Question

[manetsus]

I know that minimap and such types of tools could map read to reference. But which tools are using this mapping as input?

Could you please provide a list of those prominent tools?

[GenoMax]

See the variant callers listed in this paper.
Similarly search for tools that do functions listed by @Harold in the other thread you had about this.