View Full Version : Getting FTDNA's haplotree updated for R1a

01-02-2017, 04:27 AM
I'm not R1a but I noticed on another forum a person concerned about some of the Big Y results and how they are affecting his R1a haplogroup label.

I can't speak to that specific case but I want to make sure you are all aware that FTDNA has has a dedicated haplotree maintenance guy for the last couple of years. I just found out about him this summer and have been very happy with his work.

He has an excellent tool set and can easily and quickly evaluate low level detail (i.e. times coverage, ambiguity, etc.) of BAM results for given SNP locations. Since he has access to all Big Y BAM file results along with SNP Pack and single SNP testing results he sometimes sees things we weren't aware of as project administrators.

I've had great success looking at something in R1b we call the Big Tree, checking YFull and FGC tree info and then submitting requests for new branching or branch repositioning. As I said, since we may not have all of the BAM files, some times FTDNA comes up with greater refinement in branching.

It's important to recognize that FTDNA has a two layer process for SNP results. They have an automated process that is very conservative and somewhat dumb. They use this to build the VCF files and to initially populate FTDNA account "Haplotree & SNPs" updates and haplogroup labels.

However, haplotree maintenance requests are treated similarly to FGC or YFull interpretations in that direct review of the BAM files, phylogenetic consistency/conflicts, and other things like homologies are checked. This is free, but it is request driven. Michael Sager is the guy for project administrators to work with. He also can force a haplogroup label update. For instance, you might have a guy with a low coverage derived (but rejected) call and if Sager sees the phylogenetic consistency is there he can force the derived result to appear and affect the haplogroup label.

01-02-2017, 01:57 PM
Thanks Mike,

we will have plenty of work to deal with submissions but it's good to know, that there is someone competent on the other side and our words will be heard properly.

From what I've seen roughly a month ago - some of the Big-Y tested project members seem to be included in freshly-added branches.
I don't know who made the request in their case, maybe @lgmayka? But I have doubts about that. Some of them have SNPs with different names (from -BY series) than those used with the YFull and an R1a Project (-YP and -Y series) . It may be an unknown submission from one of our testees, I guess.