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Family Finder Advanced Topics Advanced discussion about Family Tree DNA's Family Finder Product.

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  #1  
Old 26th January 2014, 02:36 PM
1_mke 1_mke is offline
mtDNA: K2a | Y-DNA: R-L1029
 
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Phasing

For those of us lucky enough to have at least one parent available it's possible for our files to be phased such that every pair of SNP's is ordered consistently. IE,

MF
MF
MF
MF

Rather than randomly

FM
MF
MF
FM

F=Father
M=Mother

I'm thinking the main reason this isn't done is that most of the matching programs today assume that the pairing order is random. It seems though that matching would be much faster if the programs doing the matching could assume a consistent order for the SNP's in two files being compared.

Am I understanding and describing this correctly?
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  #2  
Old 26th January 2014, 02:53 PM
hansonrf hansonrf is offline
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Location: Pennsylvania, USA
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They are reported in alphabetical order, not mf and not fm. The test cannot tell from what I understand.

Bob H.
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  #3  
Old 26th January 2014, 05:05 PM
1_mke 1_mke is offline
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True, the test can't but if you have at least one parent who tests you can figure out which of the pair of chromosomes came from which parent and put things in the proper order, or so I think. Matching at that point becomes much easier as you don't have to assume that the ordering is essentially random.

Of course crossover events would still have to be accounted for but you'd no longer need to account for one with every single SNP.
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  #4  
Old 26th January 2014, 08:43 PM
S9 H9 S9 H9 is offline
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If both you and the one parent are heterozygous at a location then a unique assignment cannot be made.

Note also that there are utilities that will attempt to phase your SNPs based on a group of people, rather than your immediate family members.
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  #5  
Old 27th January 2014, 06:26 AM
JSW JSW is offline
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Location: San Antonio, TX
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The program having to account for MF vs FM is such a small part of the
problem of matching that even looking for the case where
you have ordered SNPs would remove any advantage.

Since there are such a limited number of possible matches
and the test has been really worked on to make it fast

One way - I am not sure how it is done in any of the systems as I
did not code them - is to covert the the ACGT code to bits
and then use the logic test of AND of the two together
If the result is non zero you have a match.

Allowing for certain number is mismatches in a segment is
more of a problem than the matching process SNP by SNP
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  #6  
Old 27th January 2014, 08:31 AM
1_mke 1_mke is offline
mtDNA: K2a | Y-DNA: R-L1029
 
Join Date: Feb 2012
Location: USA
Posts: 586
Thank you everyone. I'm starting to get a better grasp of the situation.

If both SNP's are the same at a given location does it matter which came from which? You can just assign one to each and be done, right?

This stuff makes my head hurt.
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  #7  
Old 27th January 2014, 12:01 PM
JSW JSW is offline
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Quote:
Originally Posted by 1_mke View Post
Thank you everyone. I'm starting to get a better grasp of the situation.

If both SNP's are the same at a given location does it matter which came from which? You can just assign one to each and be done, right?

This stuff makes my head hurt.
That is correct and that will take care of about half the SNPs.
And many of those will be the same for people from your same background.
It is the heterozygous SNPs where they make the difference is the match.
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  #8  
Old 2nd April 2014, 11:46 AM
Canyon Wolf Canyon Wolf is offline
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Quote:
Originally Posted by S9 H9 View Post
Note also that there are utilities that will attempt to phase your SNPs based on a group of people, rather than your immediate family members.
Oh, please share with us the name(s) and location(s) of the utilities!
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