Most Federal Agencies follow a multi-step process for competitive vacancy announcements. First, an individual in the Agency makes a determination to see whether the applicants in the package are "minimally qualified". Second, the list of minimally qualified applicants are sent to a Ranking official to be ranked. Third, the ranking official sends the certificate of eligibles to the selecting official for selection. That is a VERY GENERAL description, and the process can differ widely from Agency to Agency or even within an Agency.
The portion of the process you are asking about - the minimal qualifications determination - is done in a variety of ways. Some Agencies follow a pretty objective checklist/point system. Other Agencies have a person with experience in the position make the determination. Yet others have some inexperienced HR person make their best guess-timate of minimal qualifications. My Firm has handled several of these cases, and I have seen all sorts of minimal qualifications processes - some good, some bad.
That being said, if you feel that you were minimally qualified for the position - in other words - met the KSAs (knowledge, skills and abilities) tests that were listed in the Vacancy Announcement, and you feel that you were not in the pool of applicants to be ranked because of some form of discrimination, you may file an EEO Complaint with an EEO Counselor in that particular Agency. Most Federal Agencies have their EEO Counselor contact information posted on the main agency/bureau website.
It will be difficult to prove that you were discriminated against in a "minimal qualifications" selection case, because the key ingredient, knowledge of the protected class, is almost always absent. However, you should contact an attorney that is familiar with the Federal government's administrative EEO process to determine if you have a meritorious legal claim.