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Phasing Yourself

Roberta Estes

Do you ever have one of those “lightbulb” moments?

I do.

I was wishing there was a way at GedMatch to compare everyone against me and my mother at the same time – to see who we both match.  And then I realized….there is….but not in the way I had been thinking.

Both of my parents are deceased now, but my mother swabbed before she passed over…a gift I thank her for daily.

GedMatch provides a Phasing program, under Analyze Your Data.

I used the Phasing program to recreate my father whose DNA hasn’t been available from him since 1963.  I had my DNA and my mother’s autosomal DNA results, so the phasing program compared those two files and split my DNA in half and created a “half” file that is my mother and the remainder “half” file that is my father – or at least the half of him that I received.

I looked at the Mom half file and thought to myself that I should delete it to make space since I have the whole Mom file.

I’m glad I didn’t, although I could certainly have recreated the file, because it’s that phased half Mom file that is the equivalent of running my matches against me and Mom together to see which of my matches match us both.

And the clear benefit, of course, is that I know immediately which side of the family my matches are from.  Plus, if anyone doesn’t match me and a parent, then the results are not IBD, identical by descent.  Phasing against a parent is the gold standard in determining IBD vs IBC or identical by chance.

Let’s take a look at the match results.  Please note that 1500 is the GedMatch display limit, so when you see 1500, it means more than 1500, but you have no idea how many more than 1500.  By running your two (maternal and paternal) half phased kits, you can obtain up to 3000 instead of being constrained by the 1500 limit.  In order to see more than 1500, you can sort several columns in highest to lowest and lowest to highest order, and often you can obtain the entire list by sorting the columns and copy/pasting to Excel, so long as the entire list isn’t over 3000.

10 cM 7 cM 5 cM
Full Kit 825 1500 1500
Mother Half 145 495 1500
Father Half 583 1143 1500
Total 2 Halves 728 1638 3000
Not IBD 97 >138 unknown

Truthfully, I was surprised to lose 97 matches at 10cM by having them match neither parent.  That’s about 12%.

The other tidbit you may find interesting is that I have so many more matches on my father’s side than on my mothers.  My mother’s four grandparents were Dutch (the immigrant off the boat), Brethren (endogamous, German), German (immigrant off the boat) and Acadian/English (here since very early 1600s, endogamous).  My father’s ancestors have been in this country for hundreds of years – all of them.  The German, Dutch and French aren’t nearly as well represented in the DNA data bases as are the traditional colonial Americans who had lots of children and moved west, into Appalachia leaving lots of descendants today trying to sort through their ancestry.

So, if you have one or both of your parents’ DNA, phase yourself at GedMatch.

For those of you who don’t have parents available, but do have other relatives, try the Lazarus tool to reconstruct part of an ancestor’s genome.

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