Hi, Aurora. (Aurora's going, "Not this guy again...") I'm not shadowing you; honest. But on G2G I follow most tags related to DNA.
If it's a yDNA test, GEDmatch can't accept those, in any format. I don't know if that will ever change, but it's been that way from the start. In large part it's because the most common yDNA tests--the ones referred to as "37 markers" or "111 markers"--examine STRs (short tandem repeats) along the chromosomes. Our direct-to-consumer autosomal tests for genealogy don't look at STRs: for the chromosomes that recombine, STRs are great for identifying individuals (as in forensic and paternity cases) but they can change with each generation and really can't be used beyond the parent/child relationship.
Our AncestryDNA, 23andMe, MyHeritage, and FTDNA Family Finder tests all look at several hundred thousand SNPs (single nucleotide polymorphisms, individual alleles among our 3.2 billion base pairs; around 4 to 5 million SNPs may be different in your genome compared to someone else from the same continental-level ancestry). GEDmatch accepts only these types of test results...at least for now.
The Y-chromosome thorough SNP test is a (well, somewhat) full sequencing; the most popular is the Big Y test from FTDNA. It targets almost 24 million base pairs for examination, and the results come in the form of what's called VSF and BAM files. A lot of data; the BAM file will be about a gigabyte. While there are a few third-party resources you can upload these data to--like YFull and Alex Williamson's The Big Tree--GEDmatch can't use them.
There is another website, mitoYDNA.org, that was created to help with yDNA and mtDNA matching, but it can accept only Y-STRs up to 111, and only HVR1/HVR2 mtDNA results. It unfortunately hasn't gained a great deal of traction, to a large extent--my assumption only--because FTDNA used to have more competition in testing those uniparental DNA types, but nowadays only YSEQ in Germany offers similar testing; they have no matching services, though.
There are only a little over 1,800 sets of yDNA test results at mitoYDNA.org, and over 85% of those come from FTDNA, where matching is already provided. A benefit of mitoYDNA.org, though, is that you can view the actual STR values of your matches. FTDNA doesn't show that information unless the kit number is part of one of the volunteer-run Group or Surname Projects. A caveat there, however, is that it isn't as straightforward to assess the STR values as many people assume. Unlike autosomal DNA, it isn't a binary match or non-match, and what looks like a difference at one STR that you might think represents a genetic distance of 1, may actually be a distance of 2 or 3. Being able to see the actual STR values is quite useful, but you need to know how to interpret them. mitoYDNA.org does have a comparison function that lets you compare up to 24 kits to include genetic distance, but I've never seen any explanative detail about the comparison methodology or algorithm they use, or if it attempts to take into account estimated mutation rates: some Y-STRs have a glacially slow mutation rate, and others are so variable that it isn't unusual to see them change in just one or two generations...or even back-mutate.
More than you ever wanted to know, but there's the skinny on why yDNA results can't be uploaded to GEDmatch.
