Overlapping Segment Mapper

The purpose of this tool is to provide a flexible way to show specific DNA segment overlaps in a graphic chromosome-style chart. For a detailed look at a single chromosome try my one chromosome mapper and if you want to paint a picture of which ancestors your DNA comes from,  use my ancestor chromosome mapper.

The segment mapper will make a picture of the segment overlaps from up to 40 people in the CSV file you provide which is a list of your DNA match names and their overlapping segment information.  Try it here: http://kittymunson.com/dna/SegmentMapper.php

Sample Output from Segment Mapper

Sample Output from Segment Mapper

A suggested usage is to download your FIA file from DNAgedcom; remove your immediate family, and then sort descending by the largest segments (genetic distance).

It can use almost any downloaded CSV from the main testing companies as is or sorted. Mac users getting errors please read the article on creating a CSV for some solutions.

There are four tracks used (but you can make it any number in the requesting form so 5 or 6 or …) on each chromosome display which are assigned in the order that the people are listed. So the third person gets track 3, the fifth person goes back on track 1 unless you have specifed more tracks. When overlapping segments end up on the same track the program shows what it can; you may prefer to reorder the people in your file so that overlapping segments end up on different tracks or just use more tracks. N.B. to see a specific chromosome in more detail, try the One Chromosome Mapper.

It was difficult to find more than 20 distinct colors that would work for even the color blind. So to go to 40 people I used a diagonal striped pattern when reusing the same 20 colors. Please let me know if any are difficult to tell apart.

Because the image created is html and images, you can cut and past it into an email but it is best saved via a screen shot (depress alt key and print screen) or save as a web page. The mouse-overs will not display unless you save it as a web page in which case you will also need the image files to see the stripes. Click here to download them in a zip file: stripeff99cc.zip. Put this zip file in the same folder as the saved webpage and then remove the stripeff99cc from the end of the folder name when extracting the images.

The Segment Mapper requires the column headings and contents as listed below, case sensitive, in any order, in your CSV spreadsheet

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

Column name Alternate Name Must Contain this Data
Comparison MatchName
or any column name you specify
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
SegmentStartInMegaBasePairs
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
SegmentEndInMegaBasePairs
The ending number for the segment (see above comment).
cMs Genetic Distance
centiMorgans (cMs)
SegmentLengthInCentiMorgans
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 sometimes put a note 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 a match name 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.



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

 

 

25 Comments

25 thoughts on “Overlapping Segment Mapper

  1. I have a 23andMe FIA file from DNA tools (http://www.dnagedcom.com/), in .csv format. I get a message “Input file is not in comma separated format please save as a CSV file.”

    Opening it in a text editor, I see it is separated by semicolons. Is there any advice as to how to convert the semicolons to commas? I do not have Excel on my Mac, but use Libre Office Calc.

    Thank you.

    • Hi Kitty, just got back to this. Thanks for adding the semicolon option. It doesn’t give me that error any more, but now says:
      –> Column heading Chromosome is required.
      –> Column heading Start is required.
      –> Column heading End is required.
      Please fix your CSV and try again

      I’ve reworked the file so all information is in the 5 columns.
      – Comparison column has Last Name, First Name of match, all in one column (previously in two).
      – Columns are titled (case sensitive): Comparison, chr, Start, End, cMs (all aligned left, for good luck)
      – I removed columns with my father’s name (the person being matched to), and a # SNPs column.
      – I reduced the matches to 40 lines.

      I still get the above error message. Any advice?

      Thanks for any help.

        • Thank you for catching that. I changed it, still no joy. Changed to “Chromosome” and no dice with that either. Double-checked all spelling.

          I will take a break on this for now, other duties are calling. Thank you for your help and providing this tool. I’ll try again another time.

      • I sent you an email requesting that you send me the CSV so I can see what is wrong. Are you on a Mac perchance? You can send it to me kitty at kittycooper.com

  2. It works as advertised. Being able to assign the tracks will be useful.
    I downloaded my ftdna results from DNAgedcom. I sorted based on segment size to delete segments smaller than 3cM. I suspect the little ones are IBS and clutter up the display. I then did some gymnastics to sort the file according to greatest sum of shared DNA per person. I wanted to include the 8 relatives that I knew along with the 32 folks that had the greatest sum of shared DNA. So I copied to another sheet the entries that matched my goal, deleted the rows that I didn’t want, saved as a .csv file.
    Thanks for your great tool!

    • Jim,

      Even after deleting out segments smaller than “7 CMs” I still end up with over 500 matches. The largest being about 50 cMs. I would have to map 40 at the time. What I decided to do was delete all matches from the primary gedcomdna.com utility file greater than 7 cMs, then sort by Chromosome smallest to largest. I then cut and pasted the matches for each chromosome to a separate spreadsheet, sorted by cMs largest to smallest, added the appropriate column headings, and saved as a .csv file and ran Kitty’s mapping tool for each chromosome.
      I stilled ended up with more than 40 matches on some chromosomes and the results end up a little cluttered.

      Thanks Kitty for a great tool!

      David

  3. “TextWrangler” is an excellent and free text editor that is available in the app store.

    The apple application “TextEdit” can also be used as can the OpenOffice/LibreOffice word processing app. The thing is that you need to specifically save as *.txt. You use the “Edit” “find and replace” function.

    The OpenOffice/LibreOffice spreadsheet can also be used with the save as “*.csv”

  4. Kitty, your instructions said:
    “A suggested usage is to download your FIA file from DNAgedcom;… ”
    Searching for the DNAgedcom web site got me the “DNA Tools” website. Is that where I’m supposed to be?
    I clicked on the Members tab and selected View Files. There was no FIA file listed, just:
    23607_ChromosomeBrowser.csv
    23607_Family_Finder_Matches.csv
    23607 _ICW.csv

    Where should I look for an FIA file?
    Thank you.
    -Bill Martin Denver, CO

    • When you download your data from 23andme one of the files is called FIA which stands for Family Inheritance Advanced. That file has all you overlapping DNA segemnets with the people you are sharing with

      • I meant to say the 23andme tab on DNAgedcom which yes is the DNA tools website. The files you listed are from Family Tree DNA and the Chromosome Browser file should work with this tool once you change the headings.

  5. After a few days studying, played around with both your chromosome and segment tools to get the picture I wanted this afternoon. The segment tool actually gave me the pic I wanted, the combined chromosome info to a match shared by myself, my mom, and my mom’s 2 maternal aunts. TY

    But now, I guess I’m bordering elderly at 56, can’t get the web page to print, can’t copy to print, maybe just too tired after 8 hours of work and need the instructions simpler so I can save the info somewhere for later use.

    TY though, for this tool
    Linda

  6. Congratulations on getting the picture you wanted Linda! So sorry that it does not print. That surprised me too when I tried it.

    You need to do a screen capture and then paste that into a word document or an image file. If the whole picture fits on your screen then try the print screen button. Pressing the alt key and the print screen at the same time saves the current screen image to your clipboard also. If you google “screen capture” you may find something to use with your computer and browser. I use Fireshot with Firefox for this purpose.

    • If you want to save the image for later review then why not save it to your computer?

      You can do that by right clicking on the page and click the save page as web page or the equivalent in your browser. If you have more than 20 relatives shown then you also need the zip file of striped images which is linked to from the bottom of the page – http://kittymunson.com/dna/stripeff99cc.zip

  7. Great tool! I’m having a slight issue with some folks not showing up on the graphic. I have a file with 40 people. Everything is labeled correctly but some of the people listed in the csv file and also listed in the segment “key” don’t show up as bars on the chromosome graphic. Most seem to be left off at random and they are not hidden under any others. Even after re-ordering the file, the most that would show a bar was 32 people.

      • Lisa, I think you forgot to check the box that says your data uses decimal numbers. When I checked that your csv worked fine.

        Because I mix the two myself, it figures out when it sees a period that that line is decimal. The problem comes when there is no period and it is decimal! So for example your cousin at 140 on chromsome 2 had no decimal so that became too small a segment to show up.

        If you forcefully make that column a format with one or two decimal places that would also solve the problem.

  8. Pingback: What Else Can I Do With My DNA Test Results?

  9. Mine does not look like yours at all. Its jumbled and very hard to read. Yours has a nice column down the side, mine has names at the bottom of the screen and a bunch of very small colored/striped bars at the top. Above that is what appears to be two chromosome bars with numbers underneath, the numbers are overwritten by other numbers and are far too hard to read.

    • Try sorting by segment size so the 40 people with the longest DNA segment matches to you are the ones that get graphed. If that does not work send a screen shot and the CSV to kitty at this website name without the blog. in front

  10. Kitty,

    I just noticed a quirk that may affect those who, like me, have Irish families. If you put an apostrophe in your match’s surname, like O’Sullivan, it disables the hover function. If you remove the apostrophe it works just fine.

    Thanks for this great tool. Hope it comes to Gedmatch soon.

    Jim

  11. Hi Kitty. I came across this tool and it looks interesting. What do you do with the genetic information that is uploaded to your site? As you know, sharing personal genetic information can be quite a dicey subject. Is a stand-alone version of your program available for download?

    Thank you!

    Trevor

  12. Trevor –
    I do not keep these files. They are stored as temp files on my server and get deleted soon after being used to create these images. If you have PHP available on your computer, then you could use the version stand alone. Email me privately kitty at kittycooper dot com if you want that.
    – Kitty

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