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View Full Version : Phylogenetic tools to analyze combine FTDNA Big Y and FGC Results



Pallama
11-18-2019, 09:55 PM
Hi.

I'm pretty new to Genetic Genealogy but I am technically strong.

I am trying to put together a phylogenetic tree of some men with a common male ancestor circa 1400 who have taken Big Y 500, Big Y 700 and FGC tests.

FTDNA Big Y site has started to do a nice job of block trees of Big Y results based on Alex Williamson's ytree.net, but I also have some participants who took FGC Y-DNA test and I am having a difficult time combining them.

I have access to BAM VCF and CSV (including STRs) for the Big Ys, although some are 500s and some are 700s. I have access to the FGC subscribers output files (tab, out, printable xls etc)

The problem I am having is twofold:
1) combining them and figuring out where to place the FGC subscribers and
2) Big Y seems to be dumping a bunch of men (6+) into tight group with private variants and I suspect some of them actually share variants.

Can anyone recommend an approach to create a composite tree and list variants under nodes?

Any advice appreciated

Pallama

JamesKane
11-20-2019, 12:30 AM
How comfortable are you with a *nix command line? I have some things published on my blog to normalize the BAMs and joint genotype them.

If this isn't your cup of tea, pay FGC to perform their BAM analysis on the Big Y's. The haplogroupCompare files will include something quite similar to doing the joint-genotyping yourself.