Quick answer: Use a comma before "because".
If you want meaning no. 1 (see below), don't put a comma before "because" (keep the dependent clause as restrictive). If you want meaning no. 2, use a comma before "because".
Ambiguous sentences are the best, no?
Is there any way to remove the ambiguity in this sentence?
Yes, there is. Okay, let's assume the full sentence is just "I know you didn't get the job because of your qualifications"
1. Something did not happen because of event A but happened because of event B.
Son : Dad, I've got the job.
Father : I know you didn't get the job because of your qualifications.
Here, what you want to say is that the son got the job because of some other reason.
Father : I know you didn't get the job because of your qualifications; you got the job due to the recommendation of the minister.
The ambiguity is gone because of the semicolon and the part in italics, which adds clarity. Even without the clarification (i.e., the part in italics), the sentence would have this exact meaning. Why? Because the dependent clause, that is "of your qualifications", is restrictive and has not been set off by a comma.
The dependent clause is restrictive:
I know you didn't get the job because of your qualifications. {Note the absence of comma before "because"}
The Chicago Manual of Style Guide (17th ed.) gives an example:
A dependent clause that follows a main, independent clause should not be preceded by a comma if it is restrictive—that is, essential to fully understanding the meaning of the main clause
- He wasn’t running because he was afraid; he was running because he was late. {Note the absence of the comma before "because"}
6.25: Commas with dependent clauses following the main clause
Now let's get to the other meaning.
2. Something did not happen, because of event A.
Father : I know you didn't get the job because of your qualifications; you've got a really bad GPA.
Here, a comma before "because" is not necessary because the part in italics adds clarity. If the part in italics is not provided, then you should use a comma. If this is the meaning you want, then you need to set off the dependent clause as a non-restrictive clause; that is, you need a comma before "because".
Father : I know you didn't get the job, because of your [poor] qualifications.
Alternatively, you could rephrase it:
Father : Because of your [poor] qualifications, you did not get the job.
Here is the example from the Chicago Manual of Style:
If the dependent clause is merely supplementary or parenthetical (i.e., nonrestrictive, or not essential to the meaning of the main clause), it should be preceded by a comma. Such distinctions are occasionally tenuous. In the ... example below, the meaning—and whether the subject is running or not—depends almost entirely on the presence of the comma:
- He wasn’t running, because he was afraid of the dark.
- Because he was afraid of the dark, he wasn’t running.
Therefore, if you want meaning no.1, don't put a comma before "because" (keep the dependent clause as restrictive). If you want meaning no.2, use a comma before "because".
If you still feel hesitant about the comma or the whole thing, you can just fully rephrase the sentence. You could say it like this:
The fact that you got the job has nothing to do with your qualifications.
It is not your qualifications that got you the job, but the letter from the minister.
The only reason you got the job is the letter from the minister.
