Tuesday, January 24, 2017

Working on Identifying larger segment matches

I have been mapping my DNA segments to specific contributing ancestors for a little over 2 years now.  It is something I really enjoy doing but at the same time it can be very frustrating.  When I first began I was the only one in my family who had tested.  A few months after getting my results I bought a test for my Mom who agreed to test.  This really helped when her results were in and uploaded with mine to GEDmatch as I was able to differentiate between matches which were on her side and those which were on my paternal side of the family.  GEDmatch has a tool that it extremely useful if you only have one parent who is able to test.  It allows you to use that parent's DNA to subtract the DNA they gave you leaving you with a Phased kit which containing just the DNA that the un-tested parent contributed.  Last year my sister tested and her results came in which gave me more date with which to work.  I couldn't have asked for better results.  While she is a full sister she and I match at 2513.7 cMs(not including the X amount) which is on the low end of full siblings meaning we received varying DNA from our parents.  I also created a phased kit of the DNA which she received from Dad and compared it to the phase kit of the DNA which I received.  It has given me a pretty good visual phasing though it's not perfect you can see the re-combinations.  I used this comparison to mark the segments where we were opposite and was able to narrow down some segments to PGM or PGF.

When I first got my results I was busily collecting my matches....I collected anything 5cMs and up.  I guess I thought I'd miss something if I didn't.  Sure I could have but now I am working with the larger segments and I wish I had done this in the first.   I use GenomeMate Pro to catalog my matches and keep track of the kits I manage.  Most of the time I have anything over 12 cM hidden when viewing the matches on each chromosome.   I thought it would be a good project to tackle some of the larger segments.   I wanted an easy way to see the larger matches across all of the chromosomes at the same time. Below is what I did using my paternal phased kit

  • Run a Matching Segment report set where it only includes 20+ cM segments
  • Paste the results into a spreadsheet
  • Format with headers to your preference 
  • Set the sorts so it will sort by Chromosome and then by starting point
  • Use the fill cell tool to group the ones which cover the same area
  • Add a column on the far right of your Spreadsheet.  This column will be used to identify whether the match or the match group is from the Paternal Grandfather or the Paternal Grandmother's lines.

 How my chromosome, starting and ending position and segment size groups look
minus any identifying info(GEDmatch #s email addresses cropped out of pic)

I did the same thing using the paternal phased for my sister.  Yesterday I printed the spreadsheets and put them in  sheet protectors in a binder.  Today I begin reviewing our largest unassigned segments.   Technology is great...but I really do better if I have a printed paper to look at while searching over a pedigree chart rather than flipping back and forth from the chart to an actual spreadsheet or program.  Just the way I'm wired I guess.  I'd love to hear what has worked for others 

This is how I have my outer column for now  I could do a reprint later as I identify
PGM or PGF lines....but for now I will edit the old fashion way
(remove from sheet protector use color pencil and pen to add info
replace in sheet protector)

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