BigY results page

[dtvmcdonald]

I do the analysis for a big project (Donald USA, about 2000 men). For BigY I try to get at least VCF and BED files, and have a self-written program that analyzes all that I have and imputes certain missing SNPs. This works great.

For my R1b participants that's usually all thats needed,
but for some R1b and all R1a-CTS4179 files (the latter are
extremely common) I need the BAM because for CTS4179 there
are three extremely important markers (one SNP and two kilobase long deletes) that need the BAM.

BUT ... not everybody sends me the BED/VCF. I've tried analyzing the FTDNA BigY results page and it seems hopeless.
Its often completely unobvious how they assign haplogroup!
There are frequently SNPs along the tree from the R root to
the haplogroup along the tree that are neither red nor green, get are clearly there in the VCF/BED or BAM.

When I try to look them up in the left hand column they are NOT THERE ... for example a common SNP is S744. IF I try to look it up I get CTS744, same for any S SNP.

What do other people do other than beg for VCF/BED files?

Can FTDNA supply a clear discussion of EXACTLY what the data on the BigY page means? I've tried support to no avail.

[John McCoy]

By all means, this information needs to be made available. If nobody currently at FTDNA knows the answer, they shouldn't be doing the analysis at all. And if they can't explain it, the results page is just jibber-jabber, not what was paid for!