GEDMatch

Each DNA kit you upload will be assigned a number, preceded by a letter identifying the DNA testing company.  The letters assigned are as follows:
A-Ancestry
E-GENETIConcept (a partner to 23andMe)
G - Generic
H-MyHeritage
M-23andMe
P – Phased Kits – not included in queries unless manually entered
T – FTDNA
W-WeGene – Users can import 23andMe and Ancestry kits and receive health indicators
Z-Kits not meeting parameters
 
You should upload a gedcom file which should contain your ancestral lines only.
 
Each gedcom cannot contain more than 10,000 individuals or 10MB.
 
Notes on GEDMatch:
Their tools do not use the same thresholds to determine matches!!  For the One to One tool results to match the One to Many tool results, the One to One SNP threshold should be 500 and the cM threshold 5cM.
 
For males, matches on the X chromosome must be a maternal match.  Sisters sharing a father will always share an entire X chromosome.[1]
 
Unidentical siblings with same mother:[2]
1. Can share the entire maternal X-chromosome from either maternal grandmother or maternal grandfather
2. Can share 1 or more portions of the maternal X-chromosome
3. Can share no maternal X-DNA
 
If the user has not identified a gender for their kit, the following test can be done with 23andMe kits only:
Take a 23andMe kit for a female and compare it against a 23andMe kit for an unknown gender using the X one-to-one comparison tool, with the graphics bar turned on.  If the color green is seen in the results, the kit with the unidentified gender is that of a female.
 
For example, Kit M085827 is for a female.  Kit M202956 is unidentified.  There is no color green in the X comparison performed, so therefore the gender of M202956 is male.
 
Notes on the Phasing tool:
It is in the blue 'Analyze Your Data' box under 'DNA Raw Data' - 7th bullet point.  You need your kit and one of your parents’ kits and it will produce two kit numbers for you, identifying which DNA you received from each parent.  The P1 file (paternal) is the one you can use to find matches to your father.  The M1 file (maternal) is the one you can use to find matches to your mother.
 
I have tested at both Ancestry and 23andme.  I did this phasing test for both kits.  I then ran my father's dna matching segment report and the matching segment report for both of the P1 phased kits (Ancestry and 23andme).  I set the criteria for all 3 matching segment reports at 15cMs.  My dad's kit matched to 13 kits other than my sister and I.  My paternally phased kits matched on 5 of those 13 kits.  While you're not catching everything, you are getting almost 50% of the matches.  It might have been more if I had set the criteria to lower than 15cM.
 
Ethnicity Estimate Tools[3]
MDLP - territories from the former Grand Duchy of Lithuania
Eurogenes - European
Dodecad - Eurasian
HarappaWorld - South Asia, India, Pakistan, Bangladesh, Sri Lanka
Ethiohelix - African ancestry
puntDNAL - African, West Asian, European
GedrosiaDNA - India
 
Definition of New Root, a 2D visualization option from the One-to-Many Tool:
New root means there is a segment which isn’t shared with the previous match.  Kit A759182 matches with Jimmy Q on Chromosome 1 & that segment doesn’t match either Cathy or myself, so it’s considered a new root.
 
Matching Segment Tool - It provides a listing by chromosome and starting position of your matches.
 
Segment Triangulation Tool - Results are shown for segments 7.0cM and larger with 500 SNPs and larger. 
Processing time may take up to 45 minutes.  Don’t refresh the screen!
Sorted by chromosome then start position
Once you have mapped a segment of DNA to an ancestor, if others match that same segment, you know the ancestor!!
 
Presentation on GEDMatch.
 
2018 Salt Lake Christmas Tour Presentation
 
 
 
[1] Blaine T. Bettinger and Debbie Parker Wayne, Genetic Genealogy in Practice (Arlington, VA. : National Genealogy Society, 2016), 103, Advantages, Limitations, and Test Strategies for X-DNA.
[2] Bettinger and Wayne, Genetic Genealogy in Practice, 104, Advantages, Limitations, and Test Strategies for X-DNA.
[3] Blaine T. Bettinger, The Family Tree Guide to DNA Testing and Genetic Genealogy (Cincinnati OH : Family Tree Books, 2016), 163, GEDmatch Ethnicity Calculators.