In a social media group, I saw an admin post there were no cons to using GEDmatch. This admin has a know everything attitude. Contradict them in a group they admin or are a moderator, you get booted from the group. I chose to not say anything as I can think of several cons with GEDmatch.
To me, one of the biggest disadvantages with GEDmatch is comparing DNA samples from different DNA companies. If you use this reference chart from ISOGG: https://isogg.org/wiki/Autosomal_SNP_comparison_chart#Autosomal_SNPs, you can see some major differences between not only different DNA companies, but even among different chipsets with the same DNA company. A 23andMe v2 chip compared to the current v5 chip only shares a bit less than 99,000 SNPs between the two chips. The 23andMe v2 chip has over 556,000 SNPs in common with other v2 chips and the v5 chip has over 613,000 SNPs in common with other v5 chips. That’s a huge difference between the two chips. I tested with the v3 chip with 23andMe. I share a lot more SNPs with a v2 chip – almost 528,000 SNPs in common with compared to just over 177,000 SNPs with v5 chip.
What the above means is I am missing some potentially strong matches with v5 chip testers. My goal is to eventually test with 23andMe‘s v5 chip as that will give me a better comparison than what I am getting with my v3 chip. I would keep both the v3 and v5 chip sets up and mark them in a way that people would recognize both kits are mine, but indicate which chip was used with each.
One advantage GEDmatch has that you can create a superkit that combines the different parts of the various DNA tests you have taken. I tested directly with all the major DNA companies – AncestryDNA, 23andMe, FamilyTree DNA (FTDNA), MyHeritageDNA, and LivingDNA. I have not tested with each chip used by the different companies, but I have tested with at least one chip from each company.
Another disadvantage is GEDmatch was recently hacked. I don’t know if it’s because they were using less than optimal passwords or something else. No online system is hack-proof. There are other disadvantages, but in some cases, people would argue a few are actually advantages.