Thursday, June 5, 2014

Chromosomal mapping of Ancestry from 23 and me

Yesterday I posted how I made a spreadsheet utilizing the ancestry composition file I downloaded from DNAgedcom. I was thinking of an easier way to use the information to determine if the matches were a possible connection to my grandfather's Choctaw relatives. Then it hit me. I could mimic the table format used by and put the data into genome mate.

The process I came up with was a bit labor intensive. In the fact that you could more easily use the minimum default values for cM and SNP totals, but I wanted it to be more accurate. Even if you don't do what I will describe below, you will get a map of the Chromosome's that will look something like this.

I searched and read for quite a while before I found the necessary instructions to find the cM data. I finally found the data on this blog. Note your eana and American results will overlap, there is no need to do the same section twice.

To figure the cM units for a segment
1.Go to Rutgers Map Interpolator.
2. Open your spreadsheet with your ancestry composition information from 23 and me.
3. On Rutgers Map Interpolator, select the Chromosome from the drop down menu.
 4. Select physical location only.
5.  Put the start number in on one line, put the stop number in the next. Either copy and paste or type.
6. Select get map positions.
7 Take the sex averaged cM's, subtract the start from the stop. This is your cM value. For the X chromosome there is no other option than female cM position. (round to the nearest tenth)

Thus on a result such as this
Map Interpolator Results
No.  Chr Query_Posn Sex_Ave_cM Female_cM Male_cM
1   9   10411338    25.6840   17.0798 34.4570
2   9   87589165    87.0749  107.9594 67.5525

The cM value would be 61.4 cM

To ensure that I had the right format I copied and pasted a result from family inheritance advanced on 23 and me  in view as a table to a blank document. I then entered the data into the table exactly  as follows. (using the above example)

Jane Doe vs. Native American 9 10411338 87589165 61.4 cM 700 

I used the default value of 700 SNP because I couldn't find a way to figure out the total of each segment. I did run across several matches where I got a NA for a result. In that case I used the default of 7.0 cM (which is why I learned this was all unnecessary).

I then took the table and copied it. 

What worked for me was to first convert the table to text separated by tabs. I then did the manual entry for 23andme data on the genome mate program. Basically you select the 23andme family inheritance advanced option on import and paste the data and hit format. Don't forget to save or backup your data before and after you do your upload.

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