Ancestor Chromosome Mapper

Brynne Ancestor MapThis program will make a pretty chromosome map from a CSV file which lists ancestral DNA segments from your known paternal or maternal ancestors, up to 20 ancestors on each side (you can have more if you specify your own colors).

The mapping tool is currently located at:
http://kittymunson.com/dna/ChromosomeMapper.php

More about it with pictures in my August 3, 2013 blog post and more pictures, including the one to the left, in this September 2014 post.

Use my other tool, the segment mapper, to make a chart of overlapping segments from relatives or possibles for up to 40 possible relatives. And use my one chromosome mapper for a detailed look at overlaps on a single chromosome.

The Chromosome Mapper requires the column headings and contents as listed below, case sensitive, in any order, in your CSV spreadsheet. It is intended as a tool for picturing your ancestral DNA as determined from known relatives as opposed to showing your DNA overlaps from unknown relatives.

Mac users getting errors please read the article on creating a CSV for some solutions.

To better understand the chromosome mapping concept, read the ISOGG wiki article on mapping. Also I have an article on making a spreadsheet of your chromosome matches on this blog.

Once you have a spreadsheet that you want to make a picture from, that sheet has to be saved as a CSV (comma separated values) text file in order for this tool to make a chromosome map from it.

Rebekah Canada has done a really nice step by step tutorial of how to use this tool with screen shots on her blog here:
http://www.haplogroup.org/chromosome-mapper-kitty-cooper/  Thank you Rebekah!

Current List of Required Columns in your CSV file for this Tool

Column name Alternate Name Must Contain this Data
side This column is optional, select which side (warm or cool colors) the segment appears on.To use it put the letter M or P or any words starting with those letters to indicate maternal or paternal side of your tree, this must be added by you to any CSV downloaded from 23andme or Family Tree DNA or DNAgedcom
MRCA Comparison or any column name you specify Most Recent Common Ancestor(s) – this is the name to use in the chromosome map picture, you can tell the program to use a different column name for this.
chr Chromosome Chromosome number 1-22 or X
Start Start point The starting number for the segment location used by 23andme and Family Tree DNA, in the 23andme ancestry these numbers are divided by 100,000 so check the box for decimal if you are using that style of number.
End End point The ending number for the segment (see above comment).
cMs centiMorgans (cMs) The number of centimorgans in the segment, used for display purposes only. Since this is for display only you can put anything in this column for example I put the relative then a dash and the cMs
Color color colors This column is optional, you can let the tool pick the colors; but if you want different colors then put any color name from this list: http://www.html-color-names.com/color-chart.php in the color column the first time an ancestor appears in your CSV. The color name must be exact and case matters. Optionally, you can use a hex color like on the first page of this tool with a # in front of the hex digits. Warning, if you use one of the colors shown, it will also be used in order for another person, fix this by looking at the result and then specifying a different color for that person as well.

Sample spreadsheet for this tool:

CousinSampleCSV

Programming is how I make my living so a small donation of $5 or $10 would be most appreciated, if you find this tool useful.

My paypal page is here: http://openskywebdesign.com/PaymentPage.html

37 Comments

37 thoughts on “Ancestor Chromosome Mapper

  1. THANK YOU!

    I have been thinking of this where to get a program, where to put the
    matches together and here it is.
    Have to try immediately next week.

  2. Kitty,
    I just posted this on the Newbie list. Thought I should post here too.

    Kitty kindly agreed to make this tool after I posted a request for a programmer to do just that. The idea behind it Is to be able to map KNOWN ancestor’s
    segments. You cannot do this by simply downloading a .csv file and uploading to the Tool. And this isn’t for the casual DNA genealogist.

    There are actually many ways the tool could be used as it allows you to label color segments and have them “plot” on a chromosome map.
    1) So you could map by ancestry composition like the Ancestry Composition tool does at 23andme but you can include stop and start points which would be
    helpful for comparing with matches.
    2) You could paint “known” segments of your 16 gg-grandparents.
    3) You can paint the MRCA segments for any match

    Basically the tool gives you the power to create graphic representations easily via a .csv file.

    Now the HARD PART. (And although I save match information getting this to work was not easy) First of all you must use a program that allows you to save a file in a .csv format which is basically comma delineated data. I could not find where to do that on my Open Office program (maybe EXCEL Office is easier to find) So I switched to using Mac program “Numbers” which allows you to save file in .csv. The suggestion above to Use Google docs is a great one.

    Now what to save. Yes you can dowload data in this format. You can download all your match information from 23andme or 5 (10 I just learned) at a time in FTDNA or use DNAgedcom.com to download from both easily. BUT that gives you all your data and matches not the ones you need or have identified. The way I have tracked data from matches is each share at 23andme I compare with known relatives and plot that info in a spreadsheet. When I know the MCRA I note that or where I suspect the connection. At 23andme I look at their ancestry composition for the shared segment for clues. If the match and
    I both share German-French on that segment that’s a clue. Over time you build up a list of identified segments and now you can use the tool to create a
    Chromosome Map.

    if you are just starting out you may not have ANY KNOWN segments thus you would have a blank Chromosome Map.

    As to the nuts and bolts. I just copied the headings directly as Kitty has them and pasted them into a new spreadsheet in the first row. Then I copied and
    pasted the data into the new spreadsheet from my tracking sheet. For some segments I did not have the cM length so I just faked a length (entered an
    estimated value) which worked fine. Chosing colors was a bit tricky as you have to place your data in a way that selects the color you want. Perhpas in later
    versions there will be an input for chosing colors.

    For those of us wanting such a tool this is FANTASTIC so Thank you Kitty! But like all tools it takes some practice to be able to use it effectively and you can’t use a paint brush without paint. So if you want to use the tool you’ll have to start the painstakingly slow process of tracking matches and identifying segments. Which brings us round to the frustration of not having matching segment data at Ancestry where I have nearly 100 identified matches!

    I hope this helps some of you understand the genesis of the tool and how to use it.
    Kelly

  3. Awesome tool Kitty. Well done.

    There is a bit of a problem for those who don’t know their parentage as it won’t run if you don’t declare a p or m in the side column. Perhaps the instructions should say “If in doubt default the lot to p”?.

    Also an add on to your documentation for Mac users, when saving from Numbers it offers 3 format choices for the csv format It must be the windows format to make it work. Also the capitalisation and spelling on the headings must be as written exactly or it won’t play.

  4. Thanks for the tool.
    My interest is taking a group of matches that I don’t know how they are related to me. So, I’d like to compare the chromosome matches one or more unknown matches to one or more known matches. By seeing where the unknowns are in common with the knowns, I’d infer who the common ancestor is.
    Perhaps in a future version, any chromosome that has overlaps from different people, the graphic would just get wider to accommodate the overlap.

  5. Help

    I do not get any results. I have exported file from 23 and me. It is accepted and when it downloads to 100%….contacting Kitty Munson. I have tried this several times.
    Thanks!

    • Please read Kelly’s comment above. Please check that your file is a CSV. You can do this by opening it in notepad or other text editor. If it is not plain English with many commas then it is not a CSV.

      I will write some documentation on creating a CSV soon since so many of you have trouble with that. It is particularly tricky on a Mac.

      Other users can create a CSV but then leave the side and MRCA columns blank and are surprised when the tool finds nothing to plot!

  6. Would it be possible to add one more column to the CSV file that would permit adding a note to the MRCA pop-up? This would allow me to give all segments from a particular great-grandparent the same color across my map, but then add a brief comment like “COOK/BIRDSALL” to only one of those segments (to pick one of my ancestral couples, way back in the 1600s, where I have identified a common ancestor at 23andMe), without exhausting the color palette.

    • Elizabeth –
      Because the number of centimorgans in the segment is used for display purposes only, you can put anything you want in that column. For example I put the relative’s name then a dash and the cMs. So try that for your comments.

  7. Kitty,
    Great job. I have a suggestion. I like the (M)aternal and (P)aternal side, but it would be awesome to add an (U)nknown option. This will make a third row on each Chro. This way the unknown is not covered by the M or P. Use a gray scale or paterns.

    • Good idea. I have also had a request to allow “Both” when an ancestor is from both sides so the third line would be “both” or “unknown.”

      I also plan an additional feature in this tool to allow up to 5 or 6 tracks, no sides, to look at overlapping segments graphically. Probably release 3 or 4

  8. I’d really like to try this but am wondering since we are uploading our DNA to your program, does that mean that you have a copy of our DNA? I was hoping that I would be able to download the program to my computer and then upload my results. Is this possible?

    • Jan you are not uploading your DNA to this program. Rather you upload a CSV version of your spreadsheet of segment locations of DNA from specific ancestors. This file is not kept here after being used for the display.

      The advantage of a web based program is that it works on Macs, PCs, tablets, …

  9. I just released a new version of the mapper which will work without a side column by randomly assigning sides.

    A suggested use is to take your FIA file from DNAgedcom and sort by largest segments and then run that file in this tool. You will see your top 20 matches.

  10. Kitty,

    First of all, thanks for this mapping tool. I feel it is going to be a valuable tool. I have two quick questions. After downloading the spreadsheet and getting the headings correct, I end up with each of my matches listed along with each chromosome they match segments on. When I find a documented connection to this person (let’s say it is Smith born 1830) do I add this MRCA to each of the chromosome matches? How do I determine which chromosome match is correct for Smith? My second question is, as I get additional matches on FTDNA FF, do I create a new spreadsheet (this overwrites all the headings etc I have prepared) or should I enter them manually?

    Thanks
    David

    • David –
      Assigning a DNA segment to your paternal or maternal side is called phasing. There is an ISOGG wiki explanation here: http://www.isogg.org/wiki/Phasing

      If you do not have a parent to test, then 1st and 2nd cousin tests can be extremely useful for phasing.

      As to whether to add an MRCA that is up to you. This is just a tool for turning data into a pretty picture of chromosomes which can be used in many different ways.

      Same answer for creating a new spreadsheet. If there is no additional data in your current spreadsheet then you can just paste in the new column headings on the new sheet. Column ordering does not matter to the tool. Personally I keep adding new data manually since I have much information in my current spreadsheets.

      I am working on a new tool now, a segment mapper, which will show up to 60 people with matching segments on five lines within each chromosome.

  11. Having run the chromosome mapping tool, where is it to be found? If execution falls over for any reason, is there any error messages?

    • I have improved the error reporting for the segment mapper but possibly not this chromosome mapper. The results appear on your screen. If they do not there is an error in your CSV file. Please check that it is a CSV and that all the headings are correct.

  12. I’m getting the error message, “Column heading MRCA is required.
    Your file is probably not a CSV file please fix it and try again.” The file is a CSV–I tried saving it as such in both Excel and TextEdit–and I do have a column with the heading “MRCA.” I checked all of the column headings for accuracy and case. I’m using a Macintosh.

    What’s wrong?

  13. P.S.: Here are the first two rows, the first version pasted from TextEdit and the second from Excel:

    side,Chr,Start point,End point,cMs,MRCA
    p,1,7414707,38986739,51.1,Baynes

    side Chr Start point End point cMs MRCA
    p 1 7414707 38986739 51.1 Baynes

    • You might try posting this question on the ISOGG DNA_NEWBIE list at yahoo. The idea of these tools is to use them as you please. Thus the answer depends on what you are trying to do. This chromosome mapper tool is for DNA segments you have assigned to specific ancestors but of course you can use it in other ways. I use the Segment Mapper tool with my brother’s data to look at known relatives, posted here.

    • Having looked at Kathy’s file here is another tip for all of you:

      When a CSV file does not work, try looking at it in a text editor like notepad to see what might be wrong.

      In her case she would have seen lines with endless commas ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

      So however she added those new lines did not work correctly, it added them all to one line perhaps

  14. Hi I did dna testing to find my dad. I have all this testing and I do not understand how to narrow it down to find him and his family. Do you have any ways for me to narrow down all these people to help me get to the one person I’m really looking for. thanks for any help you can give.

    • Another possibility if you have multiple kits at ancestry is to download the raw data for each and then use the tools at http://www.y-str.org/p/tools-utilities.html

      There is a tool called autosomal segment analyzer there which you could use after using the convert tool on that site to convert your raw data to 23andme format

  15. Yes but …. All my tools work with CSV files of segment start and stop points, not the raw data, so you would upload your raw data to GEDmatch.com once it is back to full service to get that information (and convince your closest matches to do the same)

    Alternately you could transfer your ancestry results to family tree DNA for a small fee

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