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I have Dante Labs WGS kit for which, using WGS Extract, I created an everything kit for GEDmatch. When I uploaded it as other since Dante Labs is not an option, it was identified as being "23andMe kit type V3". I did a one-to-one with an Ancestry kit of the same person and got Total Half-Match segments (HIR) = 3559.9 cM (99.260 Pct) so clearly GEDmatch has thrown away the portions that are not in 23andMe v3.

Here is snapshot of WGS Extract dialog for choosing what autosomal to generate:

enter image description here

Now there are tier1 tools at GEDmatch where I could combine multiple kits to make a super kit, so must I instead use WGS Extract to create a series of individual kits, one for each company and each version of that company, and then put them back together again in a super kit or, preferably, can I avoid all that overhead and somehow upload the everything file directly? Perhaps by selecting something other than other such as one of the list that is a WGS sequencing?

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Ignore the cM value offered by the One-to-One tool, as a cM is just a STATISTICAL APPROXIMATION, instead check the offered SNP comparison values, it should read: "100 Pct SNPs are full identical".

FYI: The SNP count offered for the comparison CAN'T exceed the SNP count of the smaller AncestryDNA v3 kit.

If you were to run the "DNA File Diagnostic Utility" on your SuperKit, and separately your AncestryDNA v3 kit, the total SNP counts should be greater for the SuperKit (Main Menu).

You could also manually create another SuperKit, using the likes of the dnamatch-tools script, assuming you have a Mac / BSD / Unix / Linux, at a push Windows box handy, with git and python installed. If you want to play, in a shell window, type something along the lines of:

# Get the Python script
git clone https://github.com/jeftreece/dnamatch-tools.git

cd dnamatch-tools/
mkdir test-data/

# Copy in your RAW files
mv ~/Downloads/*_dna-data-20*.zip test-data/
mv ~/Downloads/genome_*_v5_Full_20*.txt test-data/
ls -ltr test-data/

# Edit the list of file names in the top of the script e.g.
vi ./combine-kits.py

# Run the Script
python ./combine-kits.py
  > Done with test-data/Ancestry_....zip; positions now stored: 677208
  > ...
  > This kit seems to be M gender
  > Inconsistent calls not written: 298
  > Combined calls: 1118986
  > No-calls: 21180

# Check the file
less combined-output.csv

Then sign into GEDmatch, select the Upload option, tick a few boxes, play CAPCTHA, upload the CSV file, and the do a seperate one-to-one comparison, and the SNP counts in play should be larger.

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