UPDATE 11-AUG-2018: ALERT!! a new improved version of this tool is now integrated with GEDmatch Genesis. No CSV files required; it can be run straight from the multi kit analysis (Tier 1) see https://blog.kittycooper.com/2018/08/new-compact-chromosome-browser-on-gedmatchs-genesis/
The purpose of this tool is to paint a picture of specific DNA segment overlaps from a CSV file of your segment matches. It does not work with your raw data but rather with your uploaded segment matches spreadsheet. That file is not kept on my site after the image is created.
The secure URL of the tool is not working so use this URL: http://kittymunson.com/dna/SegmentMapper.php
This page provides documentation on how to use the tool. It can use almost any downloaded CSV of segment data from the main testing companies as is or sorted.
The two most common problems are not having the correct column headings (see below) and trying to use this tool on your raw data (that will not work).
The next most common problem is not having a correctly formatted CSV file. Try using this online tool to fix your CSV – http://csvlint.io/ – or use google docs. Mac users getting errors please read the article on creating a CSV for some solutions.
Another problem is that a segment does not display. This is because it is on the same track as another person whose segment is a complete overlap to it. Assign a track number to one or both of them so they no longer hide each other (see the column documentation for track below).
How to Use This Tool
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 will also work with the Ancestry Composition relatives file from 23andme. If you keep a master spreadsheet of your matches from the different companies and GEDmatch, this tool can make a picture from that CSV as long as you use the correct column headings. Also if you want more than 40 people, you have to assign colors to the extra folk with the color column described below.
There are four tracks to display segments (but you can make it any number in the requesting form so 5 or 6 or …) on each chromosome 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 specified more tracks. When overlapping segments end up on the same track the program shows what it can; you may prefer to use a track column to assign people to specific tracks 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|
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|
|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.|
|The ending number for the segment (see above comment).|
|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.|
|track||Track||This column is optional, you can let the tool pick the tracks which it will do in the order which individuals appear; but if you want to control which line of the graph a person appears on so as to eliminate an overlap that hides a result then you can use this column. See the example below which links to the article which discusses a “backwards” use of the segment mapper, that is mapping the descendants of an ancestral couple|
put image here
|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.|