Setup Clang-tidy code analysis for make Project

Hi all,
I have a c++ project which is being compiled using make on windows not using MSVC. the Project already has compile_flags.txt file in each directory that was created may be using some tools(IDE) and probably used for code analysis using IDE.
Now I have to use the same project setting and perform code analysis using command line only.
when I compile any specific file it also scan c++ header files and generating a lots of warnings and errors. Therefore I assume there is some problem to read project setting by compile_falgs.txt and it generates header errors.
can someone guide me how can I avoid these header files to scan my project.
or may be provide some solution as how can I create new database setting (compile_commands.json) for make (I dont get it from bear because I dont have MSVC project) and perform code analysis using Clang-tidy.