Wednesday, July 2, 2014

Genetic Genealogy Kit

GGK is a kit management, analysis and matching tool for Autosomal, X, Y and Mitochondrial DNA. It supports build 37 autosomal files.

Prerequisites:
Usage / Tips: When you run the first time, 'Checking Integrity of DB..' will take a while for the large download version that includes reference populations. Subsequent launches will not take longer. Open, click 'new' and add a kit by just drag and drop. To add autosomal and X (e.g, for FTDNA), just select the two files and then drag both files and drop it into the grid view. After autosomal, add ySNPs and mtDNA details. Once all kits are added, make sure to process them. Autosomal Processing will take a lot of time, so make sure you do it over night. When the kit is phased, you need to double click on the segment in one-to-one or one-to-many matches to open phased-segment-analyzer. Deleting a kit can sometimes be very slow because, it deletes all comparison data with all other kits as well. So, it is best to disable than delete unless you want to reclaim space.

Screenshot:







Download GGK v1.2.zip (390 MB). If you don't require admixture using reference populations, you can download GGK v1.2 Reduced.zip (10.7 MB).

Other Downloads: GGK CLI Import Tool (Provides the ability to import kits from command line interface or console)

Version Upgrades: Just copy the ggk.db into the new version. You don't need to download the larger version everytime. Download the reduced version and copy/overwrite with your larger version's ggk.db. The binary executables are exactly same for both versions. The only difference is in ggk.db which contains reference populations.

Documentation: Genetic Genealogy Kit.pdf (2.46 MB)

Source Code at GitHub.

License: MIT License.

References:
FAQ
Why there is a minor difference in matching segments?
Adjust the Compare.NoCalls.Limit parameter. This parameter decides to ignore the segment if more no-calls or absent positions in the matching segments. E.g., if FTDNA tests 50 sites, and 23andMe tests 70 sites between two positions and only 40 positions overlaps, them the remaining 40 sites (70-40)+(50-40) where one segment will be represented as no-calls and thus the segment will be ignored if the parameter limit is more than 40.

After changing the parameter values, why is there no change in comparison?
When you change any parameter for comparison, make sure you check delete existing comparisons before processing,. from Autosomal -> Process Kits. To speed up things, the comparisons are usually cached, so you will not find any difference if you don't process it again.

Change Log
Version 1.2
  • Bug fixes. Better support for AncestryDNA.
Version 1.1
  • Import/Export bug solved. A few bug fixes.
Version 1.0
  • Initial release.