I think you want your file to be compared line by line, You can do that in SQL but can not say that it will be fastest process. You would have to try all option and conclude which one best suites to you.
By bulk importing it in SQL DB tables which will have a ROWID column as identity been set, and then run a command to compare
select * from #file1 Join #file1 On #fil1e.ROwID=#file2.RowID
where #file1.Data<>#file2.Data