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Archiver > AUTOSOMAL-DNA > 2014-04 > 1397623742


From: "Tim Janzen" <>
Subject: Re: [AUTOSOMAL-DNA] Need Help on Triangulated Groups or Phasingand Chromosome Mapping
Date: Tue, 15 Apr 2014 21:49:02 -0700
References: <000701cf5916$2a6e0680$7f4a1380$@net>
In-Reply-To: <000701cf5916$2a6e0680$7f4a1380$@net>


Dear Sharon,
I agree with Jim's comments in his last message. I would like to
add that I find it easiest to create the triangulated groups by sorting the
downloaded Family Finder HIR file by which people match one of your children
and which don't match that child at specific locations on the autosomal
chromosomes. See a sample file for my mom at
https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20
for%20Betty%20Janzen%20(public).xls. To create this file you sort first by
chromosome, then by either or not the child shares the same HIR with your
match, and then by start position. It doesn't matter which of your two
children you pick for this process. The data from the 2nd child is also
helpful. For smaller HIRs, if one of your matches doesn't share the same
HIR with either of your two children, it increases the odds that such an HIR
will be IBS. In any case, you can still expect that about 25% of even your
larger HIRs that your matches don't share with either of your children will
be IBD.
I agree with Jim that you should make separate files for your
relatives. The way I do it for my mother and her two brothers is to keep a
separate file for each. My mom's file is the main file. If my mom and one
or more of my mom's brothers share the exact same HIR with one of their
matches then I enter the data about that HIR only in my mom's spreadsheet.
If someone shares and a HIR with one of my mom's brothers but not with my
mom then I enter that information into the appropriate brother's file.
Since you have 3 siblings, you can do this same process. What I would do if
I were in your position is to make your file your primary file. Then pick
one of your siblings as your 2nd priority file. Any HIRs that this sibling
shares with a match are entered into the second spreadsheet unless they have
already been entered into your spreadsheet, in which case they aren't
entered into the 2nd spreadsheet. You then pick another of your siblings
for the 3rd priority file. Any HIRS that this sibling shares with a match
are entered into the third spreadsheet unless they have already been entered
into your spreadsheet or that of the 2nd priority sibling. Finally, with
the last sibling you enter HIRs into their spreadsheet if someone matches
them and none of the other 3 siblings. You could eventually merge these
spreadsheets if you want to, but if you do so, you need to make sure you
keep the file sorted by which sibling shares the HIR with a match or it will
get really confusing for you. Between the 4 of you, you should have
preserved about 93% of your parents' DNA.
You are incorrect when you said that can't phase your data because
your parents are dead. You certainly can phase your data. You have two
children. You can phase 84% of your data using the data from just one
child. If you test your spouse and include his data in the phasing process
then you can phase 94% of your data. You can create a chromosome map of
your data similar to what I did with my mother. See
https://dl.dropboxusercontent.com/u/21841126/phased%20genome%20of%20Robert%2
0and%20Betty%20Janzen%20(public).zip for an example of this. You will use
your first cousin's data in the initial mapping process. This cousin will
share about 10%-15% of their genome with you. When you are done with the
mapping you will have determined where about 10%-15% of your DNA has come
from (paternal or maternal). Testing more first and second cousins will
allow you to increase this percentage. You can also phase your sibling's
data if they have children. If none of your siblings have any children,
then phasing their data will be more challenging, but you can at least
partly do it using your phased data. You will eventually want to create
chromosome maps for each of your siblings, at least for the portions of
their DNA that you don't personally have.
If you use your child's data as I mentioned above then you don't
need to worry about any long "overlapping segments" because you won't have
any. You will have already created your triangulated groups. However,
there can be short portions of an HIR (usually less than 1 cm) that are IBS
where your matches can overlap. I posted a message to the list about this
issue on April 4.
Sincerely,
Tim Janzen


-----Original Message-----
From:
[mailto:] On Behalf Of Sharon Clark
Sent: Tuesday, April 15, 2014 6:50 PM
To:
Subject: [AUTOSOMAL-DNA] Need Help on Triangulated Groups or Phasing and
Chromosome Mapping

I can never phase my information because my dad has been dead since 1984 and
my mother passed away in 1997. I have had both of my sisters participate in
Family Finder, and our brother is in the process. I have also tested my son
and daughter, and my granddaughter, along with our paternal first cousin.
So far I can't get any takers from our maternal first cousins to
participate.

Do I make one big spreadsheet for my two sisters, our cousin, and me, and
find all the segments that are in common with at least one of us and our
cousin?

Another thing that I am a little confused about is when someone mentions
overlapping segments. How does one know whether the part that appears to
overlap be on the same chromosome, say from the father, or if it might be
from the mother? I hope that makes sense. I am sure my sisters and I share
lots of segments. How would I know if someone matches on part of the
segment I share with a sister - how can I be sure it's the same segment and
not on the other chromosome I got from my other parent?




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