Friday, September 19, 2014

Genome Mate: 23andMe Ancestry Composition

There's a new feature in Genome Mate that will allow loading of the 23andMe Ancestry Composition (AC) file from DNAGedcom into Genome Mate generation zero base segments.

Step 1:  Download or Create AC File


The Ancestry Composition file can be downloaded from DNAGedcom or created manually.
  • DNAGedcom:  On test.DNAGedcom.com> 23andMe > Download 23andMe > Enter Email address > Enter 23andMe Password > Enter 23andMe Profile Name >  Check Run AC > Get Data and wait for it to finish processing
  • Manually Created File:  DNAGedcom is the preferred method of getting this data formatted correctly but a comma separated values file with similar data will also work or the AC file from DNAGedcom can be edited prior to import into Genome Mate to include just the desired segments.  Sample format:
Chr, Origin, Bar, Start, End, Level
chr13,north_european,1,19234747,115103150,1
chr18,north_european,2,69836,65014460,1
chrX-npar,north_european,1,2700157,154929412,1
chr6,finnish,1,30334339,33312308,1
chr18,french_german,1,8182346,63038207,1
Chr:  This is the chromosome number.  Note how X is formatted differently
Origin:  This is the label to use on the Segment
Bar:  1 is maternal, 2 is paternal
Start:  Segment start point
End:  Segment end point
Level:  This is the how the segment is to be layered with 1 being to bottom layer
Save the file as a CSV file (i.e. file name is {something}.csv) 

Step 2:  Import AC File


Every time the AC file is imported it will replace existing AC or generation zero segments. 
 
In Genome Mate > Import Data > Select Match Data Source: 23andMe > Load Ancestry Composition Segments > Select Profile Name > Select file named {email name}_{profile name}_23andMe_AC.csv


Step 3:  Set Option


Since the AC data can clutter up the display, the ability to toggle it on/off is included as an option.

In Genome Mate > Options > Check Show Ancestry

Step 4:  View Segments


AC segment data will automatically be displayed on the main page chromosome map but may be covered by segments defined from DNA matches.  Open the Segment List to see the Ancestry segments for all chromosomes:

In Genome Mate > Segments > Check Ancestry

Hovering over a segment will show it's origin.

Step 5:  Changing Colors/Swapping Bars


Since the AC bars are not defined as maternal or paternal at 23andMe, they are randomly assigned to bar 1 or 2. If through data analysis, it becomes apparent that they are reversed, the bars can be switched.  On the reversed chromosome, right click on an AC segment then click on the swap icon next to the segment color selection.


Finally note that the matches contained within an AC segments can be view on the main page by checking the Segment box.


Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Wednesday, September 10, 2014

Genome Mate: Segments Option

In Genome Mate, a segment is defined as a slice of DNA associated with a set of ancestors for the current profile person selected.  Segments are a way to defined what DNA for the profile person was inherited from which of their ancestors.

Let's first describe how to set up segments then move on to the Segments Map.


Creating Segments


Segments are created automatically when on a Match Details page, the ICW is set to start with M for maternal or P for paternal, AND the confirmed ancestors (MRCA) for that match are selected.

This creates a temporary segment that will be shown on the chromosome map at the top of the main page and on the Segment map.  Note that confirmed ancestor selections are only available if a gedcom has been uploaded for the profile person (Profiles > Select Profile > Load Gedcom File).

To view segment information, on the Main page, right click on the segment on the chromosome map and the Segment Details page will be displayed showing the surnames associated with those ancestors and the matches that were used to create the segment.


Segments Detail Page

A temporary segment is created when setting the ICW and confirmed ancestors on the Match Details page.  If that information is changed in the Match Details page, then the temporary segment will also change.  

When you are confident of a segment's definition, make it permanent by clicking on the Save button and you will be given the option of naming the segment id and marking the ICW of other associated segments with the segment id.  You may also add comments to the segment description.

Use the Delete button to remove permanent segments no longer wanted.


Segments Map


Segments Map
To access the Segments Map, on the Main Page click on Segments.  This displays the segments for all 23 chromosomes in either a map or table format.  To manually add a permanent segment, click on the Add Segment button and fill in the information.



There are times when mapping an ancestor is desired but intervening ancestors are not known as in the case of adoptees or in trying to push through a family tree dead end.  Adding a manual segment allows for the identity of the known segment.


Final Comments


Some thought needs to be given to how to use permanent segments and how to assign segment ids.  It took me several attempts to settle into what was acceptable for my data.

It is recommended that you backup your database and experiment before settling on a particular course of action.

Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Monday, July 28, 2014

Genealogy: The Paper Trail

DNA genealogy research is painstaking, detailed analysis of both DNA matches and the paper trail to confirm shared ancestors.  Excluding adoptees, about 90% of the matches with whom I share DNA have not put together a basic family tree so trying to find a common ancestor can be difficult.  This blog is dedicated to the paper trail.


Getting Started


First, get a genealogy program like Roots Magic to record your findings.  Starting with yourself and moving backwards generation by generation, try to answer these questions:

Who was this person’s parents and why do I think so?
Who did this person marry and why do I think so?
Who were this person’s children and why do I think so?

Exact dates are nice to have but not necessary.  If I don’t have a date for a marriage, I assume they were married before their first child was born.  If I don’t have a birth date, I assume that males were at least age 21 and females age 18 before they married.  While this can vary somewhat, it puts you in the right decade for evaluating the reasonableness of your research.

Source Data


It is important to answer the question “why do I think so?” with references to source material.  The quality of your sources determines the potential accuracy of your research.  It often takes more than one source to adequately establish the answer to one of these questions.  For example, before a marriage takes place, both families are probably residing in the vicinity so not only do you need a marriage record but proof that the family lived in the area at the time.

Family Search (free) and Ancestry (paid) are great resources for data but be aware of the that not all source data is equally reliable.

Sources can be classified as primary, secondary and questionable.  Most people can document the first few generations of their family with primary sources.



Primary sources while they can contain inaccuracies are often the most reliable information.  In a perfect world, we would document our genealogy with primary sources such as:

Birth, marriage & death Certificates
Census
Wills, probates, etc.
Land records - deeds, leases, etc.
Bible records
Pension records

Secondary sources are less accurate and subject to errors of memory or clerical mistakes. Some of these include:

Transcriptions, extracts, and abstracts
Bible entries predating date of bible
Events recorded at a later time
Historical narratives
Cemetery Markers
Diaries & Letters

Questionable sources are those that give you a clue to where to look but should be confirmed with primary & secondary sources.  These include:

Family Histories
Family Stories
Family Genealogies

In the beginning, I must have made all the mistakes that someone new to genealogy can make and that are too numerous to list here.  Finally, I settled into this simple but adequate approach for establishing a paper trail of my ancestors.

~ Becky ~

Copyright © Beckins LLC 2013-2014

Wednesday, July 2, 2014

Genome Mate: Import Data Page

The Import Data page is the main function for imputing bulk data into the application.  To update your database with new matches just load a new version of the input file.  Genome Mate will skip duplicate data and just add the new matches and relatives.

Genome Mate accepts data from several sources.  Some data is copied and pasted from browser pages while others can be imported from a comma separated values (*.csv) file from different sites.

The format of these files is determined by the site creating the file so it is important to select the correct option when loading.  If you have difficulty loading a file, send the file and a description of the issue in an email to support@genomemate.org.

There are two types data that may be imported:

1.  DNA segments shared with a Relative
2.  Relative specific data such as surnames, ICWs, email address, etc.  

When DNA segment data is imported, a table will be presented for you to review prior to adding the data. Please review any messages and if everything is okay, press the Add Data button.

When Relative data is imported, it will be automatically updated.  

Import Data Page

Step 1 - Select Data Source

Choose the origin of the DNA data segments to be posted to Genome Mate - 23andMe, FTDNA, FTDNA or Ancestry (relative data only).

Step 2 - Set the Criteria for Adding Matches

This criteria can be modified on the Options Page but overridden here for the current import.
  • Minimum cMs - Only import DNA segments having a cMs greater than the value shown
  • Minimum #SNPs - Only import DNA segments having SNPs count greater than the value
  • Add New Relatives - Check to automatically add a new relative record if one is not found
  • Show Duplicate Matches - Display duplicate matches in the table and rejects report

Step 3 - Select the Import Option

The import options for the selected data source will be presented.  See these links for more specific information about each:
Rejects and Summary
After the data has been processed, a table of DNA segment matches will be displayed along with any error messages.  If it looks okay, press Add to load into the database and get a process summary.

For relative data only like surnames, email addresses, etc., Relative records will automatically be updated and a process summary shown as well as a list of any rejects.  The most common problem loading Relative data is the present of a new line character in the notes field.  If this occurs, delete the data in the original file and reprocess.

Backups & Restores 

Backups are recommended before loading new data to ensure that work is not lost!

Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Tuesday, June 10, 2014

Genome Mate: Match Details Page

The Match Details page is the main page to use for documenting what is known about about a particular DNA match. It is opened when a DNA segment on the main page is selected.


Match Details Page
Before explaining this page in detail, let's take a moment to talk about how Genome Mate stores information. There are two types of records kept.

  1. Relative record - retains data about a relative such as surnames, email, family tree link, etc.
  2. Match record - retains data about an individual DNA segment match between the profile person and a relative
Ideally, there should be one Relative record and multiple Match records, one for each segment on which the profile person and the relative are related.  In practice, there may be multiple Relative records because of different key values from the testing companies but these may be merged into one record on the Relative Details page.  The matches for each company cannot be merged but duplicates are easily identified on the main page as they are colored according to source.

The Match Detail pages is for a single DNA segment match between the profile person and the relative. At the top of the page will be the relative's name, segment data and the source (23andMe, FTDNA, etc) of the match.  Starting left to right:

Column 1:
  • Relative - Name to be displayed for the Relative
  • Contact Name - free field to enter name of relative's contact
  • Phone - free field to enter contact's phone number
  • Relative Note - Note to be displayed with relative information
  • Family Tree - URL of relative's family tree with clickable link to open it in a browser window (for Windows users only as it crashes on a Mac)
  • Email - Email address of the relative's contact with clickable link to open the default email client and format a form letter (for Windows users only as it crashes on a Mac)
  • Match Key - this is a read only value showing the key for the relative for this match source (23andMe, FTDNA, etc.).  Right click to copy key to clipboard.
  • Match Note - Note to be displayed with individual DNA segment
  • ICW Group - Anything can be entered into this field to group common DNA segments.  However, if known, it should start with M for maternal and P for paternal.  There are radio buttons for quick entry.
  • Research Comments - this is a free field for entry of information or correspondence with a relative.
Column 2:
  • Profile Overlaps or Triangulated Matches - If triangulated matches are available, they will be displayed in the top box and clicking on the circle icon next to the title will toggle the profile overlaps display. Otherwise, only profile overlaps will be displayed.  Right click on box to copy to clipboard.
  • Enter Surnames - The surnames of the relative's ancestors should be entered here separated by a comma.  They will be stored in the Relative's record.
  • Surnames in Common - This is a list of the surnames found in common with the Profile person's ancestors from loading their gedcom in Profiles taking the ICW group into consideration.  Right click to copy to clipboard.
Column 3:
  • Connection Information - When a common ancestor is found between the Profile person and the relative and confirmed through triangulation on the current segment, the MRCAs can be selected here from the Profile person's list of ancestors.
  • Possible Connections - This is a list of the profile person's ancestors associated with the Surnames in Common.
  • Gedcom Compare - This opens a page to compare the Profile's ancestors to those of a gedcom from the Relative.
  • Connections Details - This is a read only box.  Hovering over a name in Possible Connections will display more detail about that person.  Clicking on the All Details button will display more information about all the names in Possible Connections. Right click to copy to clipboard.
  • Segments Overlapping - This is a read only list of relatives on the same side of the family who also have a match on the same segment of at least the minimum segment length (set in Options).  It shows common surnames between these relatives.
Bottom Buttons:
  • View Relative - Opens the Relative Details page
  • Add ICW - Alternative way to collect ICW data for 23andMe and GedMatch
  • Delete ICW - Allows deletion of ICW data for the Relative
  • Delete Segment - Delete's the current match record open
  • Delete Matches - Deletes all of the Relative's match records and their relative record.
  • Update Segment - Global update feature to set all matches for a relative to the opened match record values.  Back up your data before using this.  It will update and close the page.
  • Hide Match - Indicates whether to display this match record on the main page
  • Save or OK - Saves changes and closes page
  • Cancel - Closes page without saving

Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Sunday, June 8, 2014

Genome Mate Overview

Genome Mate is a desktop tool used to organize in one place the data collected while researching DNA comparisons. Besides data storage it has many features to aid in identifying common ancestors.  See Genome Mate Home Page for details on installation.

The purpose of this overview is to link together the documentation for each function and update it as individual pieces are available.


Main Page

Main Page with Graph Option

The main page of the application is made up of four sections:

  1. Chromosome Map
  2. Navigation Bar
  3. Filter Bar
  4. DNA Segment Graph or Table

Chromosome Map

At the top of the main page is a plot of identified common ancestors for the selected profile and chromosome.  It is generated automatically when a DNA segment has been identified as maternal or paternal AND the common ancestors between the profile person and their relative have been selected.  See blog on Chromosome Map Segments for detailed information.
  • Left click on a segment to display overlapping DNA segments
  • Right click on a segment to open Segment Details page

Navigation Bar

The navigation bar is used to access various functions and reports within Genome Mate. Starting left to right:
  1. Database:  To set up new or change between existing databases
  2. Profiles:   To set up new or change profile data including the loading of a gedcom
  3. Surnames:  List of profile's surnames with option to add alternative spellings
  4. Ancestors:  List of profile's ancestors as loaded from gedcom
  5. X List:  List of profile's X chromosome donors as loaded from gedcom
  6. Relatives:  List of Relative records imported with access to a Relative's Details page
  7. Segments:  Graph or Table of all 23 chromosomes with access to Segment Details
  8. Import Data:  Functions for importing data from 23andMe, FTDNA and GedMatch
  9. Backup:  Backs up the current database to a selected file location
  10. Restore:  Restores database from a selected backup file
  11. Options:  Set application defaults, export data and compare gedcoms
  12. Support:  Frequently asked questions and support email address
  13. Donate:  Paypal donations for application development and support on the internet

Filter Bar

The filter bar is used to determine which DNA Segments are displayed in the graph or table. From left to right:
  1. Profile Name:  Selects whose profile data to display
  2. Chromosome:  Selects what chromosome data to display for the selected profile
  3. Search:  Searches relative names and match keys 
  4. Surname:  Searches relative surnames
  5. Maternal:  Displays DNA segments with 'M' as first letter in ICW group
  6. Paternal:  Displays DNA segments with 'P' as first letter in ICW group
  7. Both:  Displays both Maternal and Paternal segments
  8. Hidden:  Toggles if should display DNA segments that have been marked as hidden or that do not meet the display settings in Options.
  9. Source:  Toggles whether what source (23andMe, FTDNA, GedMatch, CoA) of DNA segments to display.
  10. Graph:  Toggles whether to display the graph or table.

DNA Segment Graph or Table

In this section, DNA segments are displayed based on the filter options selected.  On the graph these are the options available:
Match Details Page:  Click on one of the DNA segments to access Match Details
Reset Filter:  Press ESC key to reset filters
 Individual DNA Segment Line Options:  
Overlapping Icon:  Left click to show just segments whose start and end points overlap this one or right click to show overlapping segments page.
Profile:  Name of the profile person for the DNA segment
  ICW Icon:  Hover mouse over this icon to see what overlapping segments have relatives in common with this one.  Left click on icon to set an ICW group value for all of the ICWs on the overlapping segments.  Right click to use this match's ICW to set the value for all of the ICW's on the overlapping segments.
ICW:   This is the ICW group value that can be assigned on the Match Details page or by using one of the ICW Icon options listed above.  The ICW group must start with M for maternal or P for paternal, if known.
Chr:  Chromosome number
Start:  Start point of DNA segment between profile person and relative
End:  End point of DNA segment between profile person and relative
cMs:  DNA segment centimorgans 
Plot:  The segment plotted on the chromosome using start and end points

 Additional Resources


Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Saturday, June 7, 2014

Genome Mate: Profiles Option

In Genome Mate, data is presented from the perspective of the profile person or the person who submitted the DNA sample.  For example, in my family, I manage kits for my siblings, a maternal uncle and a paternal cousin, each of whom has a profile in the application.  The very first time, Genome Mate is opened it will require that a profile be created before continuing (Enter Profile Name > Add > Close).

Profiles Option

Profile Name

The profile name is a key field in the individual DNA segment matches between the profile person and their relatives.  If 23andMe is one of the sources for DNA segment data then it is important to enter the profile name exactly as it is on that person's 23andMe profile or change the 23andMe profile name to match before importing data.  Do not use special characters!

To change the profile name, type in a new name then Close.  All of the associated match data will be modified to reflect the new name.

GedMatch Kit

If there is also a GedMatch Kit for this profile, enter the kit #.  This is the key field required to import GedMatch data.

Load Gedcom File

While loading a gedcom file is optional, it is required for the Surnames, Ancestors, and X List options as well as to provide surname comparisons in the Match Details page.

Only gedcom file format version 5.5 with UTF8 characters is supported.  If your software doesn't support this format, try reformatting it with the free RootsMagic Essentials app then importing it.

Some common issues with the gedcom import are having multiple ancestors linked to the same person or trying to use a format other than 5.5 such as 5.5.1.  It doesn't hurt to try a different format but the app may not process it correctly.

When new family tree data becomes available, just load the new gedcom and it will replace the old data in the application.

To load a gedcom:
Profiles > Select Profile Name > Load Gedcom File > Select gedcom file > Select the person in the gedcom who is the profile person > Yes > Close
Note that the profile person must be in the gedcom.  The application strips out the direct ancestors of the profile person along with their birth, marriage, death and residence events and uses this information to populate the surname, ancestor and X donor lists.

Delete

To delete a profile, select the profile name and a Delete button will be displayed.  Pressing the Delete button will provide an option of also deleting the profile's DNA match data.
Yes:  Deletes profile and all segment matches
No:  Deletes just the profile and leaves the segment matches so they can be display in Profile Overlaps on the Match Details screen.  However, since there is no longer a profile defined, new match data for the old profile person will not be added.  (This is an obsolete feature.)

Close

Close will check to see if the app has at least one profile or if the displayed profile name has been changed then close the dialog.  Note that profile names are displayed on the first drop down list on the main page and DNA segment data is displayed for the profile selected.

Thursday, June 5, 2014

Genome Mate: Database Option

Genome Mate initially creates a database in Silverlight isolated storage but should there be a need for multiple databases or placing the data on a different drive, a separate file can be designated by selecting Database on the main page.

Database Option

Create New Database

This will create an empty database but data in your Silverlight database will be retained.
Database > Create New Database > Enter Database Name > Select location and filename for database > Save > Enter a profile name > Add > Close
The new database is ready to use.

Change Databases

This will point the application to an existing database or even a backup file as the data format is the same. Data in the Silverlight database is retained.
Database > Change Databases > Select previously saved or backed up file 

Revert to Silverlight Database

This will point the application back to the Silverlight database.  Data in the file currently being worked will be retained.
Database > Revert to Silverlight Database

Backup

Remember that data is stored locally on your computer so use the Backup function to save your work on an external flash drive.

Sunday, June 1, 2014

Genome Mate: Chromosome Map Segments

Chromosome Map Segments are a visual representation of the DNA segments that have been mapped to common ancestors.   It happens automatically when sufficient data has been added to Genome Mate.


 The Basics

This section will provide the information required to get the chromosome map at the top of the page to display.  It requires three sets of data:

  1. Family History File:  Profiles > Select Profile Name > Load Gedcom File > Select filename > Select the name of the profile person listed in the Gedcom > Yes
  2. Identify Segment Source:  Each chromosome is made up of one part paternal DNA and one part maternal DNA so the chromosome map segment must be identified as having come from your father or your mother.
  3. Identify Common Ancestors:   For the relatives on the DNA segment in question, identify common ancestors.
With these three pieces of information, the chromosome map segment can be created:
  • In Genome Mate > Click relative's match on the main page to open the match details page > Select ICW Group (M or P) > Select Confirmed Paternal > Select Confirmed Maternal > OK
Genome Mate will automatically create a temporary map segment for the match identified. If you change it, it will be automatically changed.  I use temporary segments to track a possible origin of a DNA segment when I find a common ancestor with one relative but have yet to triangulate it with another.

Some useful shortcuts:
On the chromosome map at the top of the page:
  • Left click on a segment to see all of the matches overlapping that segment
  • Right click to see what relative or relatives were the source of the segment and possible segment surnames

Working With Map Segments

The information contained in this section is entirely optional and not required for either the application or the chromosome map to work correctly.

Segment List:  On main page, Select Segments

The Segment List displays the paternal and maternal map segments that have been defined using the criteria discussed in the previous section. For each chromosome, the map segments are layered by the generational distance from the profile person.  In other words, a father's segments would be plotted first then overlayed with the grandfather or grandmother's segments and so on.  To see an individual layer, click on the generation's color in the lower right hand corner.

Export permanent map segment data by clicking on the CSV File button.

There are cases where manually adding a segment may be desirable.  For example, I have a very well defined section of DNA that is associated with my Native American heritage but zero matches on that section so I added a segment manually as a note to myself.  Using the Add Segment button will create a permanent segment in the generation specified.

Smaller map segments can also be filtered out by the Minimum Segment Overlap value set in Options.  Check the Hide Segments box to do so.

Right Click on Map Segment to View Description
Open a description of the Map Segment by right clicking on one of the segments on the map or optionally changing to a table view and selecting the segment.

The Segment Id is assigned automatically using either M for maternal or P for paternal plus the chromosome and the segment start point.  Information on the segment, the relative or relatives whose match created the map segment and the surnames associated with the MRCA are listed. 

To make this a permanent segment, click Save.  Additional documentation will be retained if added to permanent segments.

There is also the option to Mark  or set the ICW group of all segments whose start and end points fall within the map segment's range to the Segment Id.  For a relative's match to be marked, it must be on the same side of the family as indicated by an M or P in the first position of its ICW group.  This is used to filter surnames on the Match Detail page.

Not shown is the Delete button that is available when a segment is permanent.  Use this to remove unwanted segments but be aware that a temporary segment may replace it, if the underlying data has not been corrected.

Tuesday, May 27, 2014

Genome Mate: ICW, Triangulation and Overlapping Segments

The purpose of the blog is to describe ICW, Triangulation and Overlapping Segments from the profile perspective in Genome Mate as that is how the data is presented in the application.

One of the most frequently asked questions is what is the difference between In Common With (ICW), triangulation and overlapping segments.  Let's start with a definition of each in relation to the Genome Mate profile person before moving on to more details.

  • In Common With (ICW) - ICW simply means that two Relatives have some DNA in common and are thereby related to each other but not necessarily on the same segment as the profile person.
  • TriangulationTriangulation means that the profile person plus two or more people are related to each other on the same DNA segment and thereby share a common ancestor. 
  • Overlapping Segments - Overlapping segments are DNA segments from two or more Relatives whose start and end points overlap each other.

Loading data in Genome Mate is complicated due to the need to accommodate different data sources and formats.


Getting Started Guides

Here are the links to some of the Getting Started guides.  The focus of this blog will be limited to just ICW, Triangulation and Overlapping Segments.

In Common With (ICW) in Genome Mate


In Genome Mate, there is an ICW indicator next to the Relative's name and if you hover your mouse over it, it will highlight the other relatives on that segment who are related to that person.  However, it says nothing about if they are all related on that particular segment.

When a segment crosses a centromere, there is a greater chance the segment is a mismatch or IBS (identical by sequence) rather than IBD (identical by descent).  When this occurs, the ICW group on the graph will be an orange color to alert to the possibility.

The ICW group can be set to any value by clicking on a DNA segment and setting the value in the Match details page.  However, note that, if known, it should start with M for maternal or P for paternal for surname matching and chromosome mapping to work correctly.

Keyboard shortcut:  If you left click on the ICW indicator, you can mark every person highlighted with a value you enter except for those who have an * in their ICW.  If you right click on the ICW icon, it will copy the ICW group value contained in that Relative record to all highlighted relatives except for those who have an * in their ICW value.  Use this with caution since ICW relatives are not always related to each other on the highlighted segment.

There are several ways to load ICW data depending on the data source but note that Relative data must have been loaded first or the ICW data will be rejected.

  • 23andMe - The recommended method of loading ICW for 23andMe is to use the 529andYou CSV file but there are other, more time consuming and less comprehensive ways to get the data.  In order of preference:
  • On 23andMe > My Results > Ancestry Tools > Countries of Ancestry > Select Relative name > Click Download {Relative's Name}'s Countries of Ancestry Matches (CSV)
  • In Genome Mate > Select one of the Relative's DNA Segments > Add ICW >  Import Data from CSV File >Select file named ancestry_finder_{name}{date}.csv 

  • FTDNA - The only way to import ICW data for FTDNA is to use DNAGedcom.
  • On DNAGedcom > Family Tree DNA >  Download Family Tree DNA Data > Enter Kit # > Enter Password > Get Data > Wait for processing to finish > Find zipped file in your download folder and extract files 
  • In Genome Mate > Import Data > Select Data Source > Load ICW CSV file from DNAGedcom > Import Data from CSV File > Select file named {kit}_ICW.csv

  • GedMatch -  ICW is loaded when loading the segments from Segment Triangulation (see blog) but it is limited to the top 200 matches.  
More ICW data can be loaded one relative at a time by:
  • On GedMatch > 'One-to-many' matches > Enter kit number > Display Matches > Select data (Ctrl or Cmd a) > Copy data (Ctrl or Cmd c)
  • In Genome Mate > Select one of the Relative's DNA Segments > Add ICW >  Copy Data (Ctrl or Cmd v) > Format
ICW data provides clues that the researcher can use to dig further into family trees to see if there is a connection between Relatives on the DNA segment in question.  Not having an ICW between two relatives is a good way to avoid researching people not related.


Triangulation

Triangulation means that the profile person plus two or more people are related to each other on the same DNA segment and thereby share a common ancestor.  This is determined by a three way match between the profile person and two relatives (P = A, P = B, A = B).

Automation of triangulation is only available for 23andMe data imported from the 529andYou CSV file and the Segment Triangulation data from GedMatch (limited to first 200 top Relatives).  

If triangulation data has been loaded into Genome Mate then clicking on a Relative's DNA segment will show the triangulated data in the upper middle box of the match details page. 

Triangulated relatives establish an ancestral line on which they all share a common ancestor even if that ancestor is not currently known.

Overlapping Segments

Overlapping segments are DNA segments from two or more Relatives whose start and end points overlap each other.  Each overlapping segment contains DNA from both the paternal and the maternal sides of the family so segments that overlap are not necessarily related to each other.  

Use DNA matches to known family members to set the segment's ICW group to either P (paternal) or M (maternal).  Otherwise, any ICW value is okay to indicate a group of triangulated matches.

Segments that have been identified as maternal or paternal but whose overlap is small may not be related.  To to filter those out, a default overlap value can be set and compared to the segment's start and end points to determine if it should be displayed.  To set the default value:

  • In Genome Mate > Options > Set Minimum Segment Overlap

There are tools in Genome Mate to work with overlapping segments:  

  • On Genome Mate graph:  Left click on the circle icon next to the profile name and all of the segment overlaps for that particular segment will be displayed.  If the segment has been identified as maternal or paternal, it will display the corresponding maternal or paternal segments plus those that have not been identified.  This display ignores the default overlap value and shows all overlaps. Use ESC to return to a full display.
  • On Genome Mate graph:  Right click on the circle icon next to the profile name and an Overlapping Segment Page will be opened showing all of the DNA segments for all sources (23andMe, FTDNA, etc.) that overlap the selected segment by the default overlap value.  It shows the common surnames shared among those listed on the page. Clicking on a Relative in this list will open their Match details page.
  • On Match Detail page:  In the lower right corner is a list of segments overlapping the selected DNA segment by the default value along with shared surnames.
Overlapping Segment Page

The Overlapping Segment Page is my primary work space when trying to identify common ancestors as it gives a global view of the segment in question.




Backups & Restores

Creating backup files cannot be overemphasized.   Experimentation is encouraged, but make sure you have a safe harbor.

Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014

Saturday, May 17, 2014

Getting Started with Genome Mate using 23andMe Data

Genome Mate is a desktop tool used to organize in one place the data collected while researching DNA comparisons.  Besides data storage it has many features to aid in identifying common ancestors.  It can be downloaded at http://genomemate.org/



The following guide was originally put together by George Cunningham and published with his permission.  It has been edited to reflect changes in the application.


23andMe Getting Started Guide

There are three steps required to load 23andMe data:  Setting up a profile, load DNA segments and loading associated Relative data.  Under step 2, loading DNA segments, there are multiple options for obtaining that data.  Please read each carefully before proceeding.

Step 1:  Create a Profile


  • First create a profile in Genome Mate for each kit that you manage
    • Profiles > Add new profile
  • Put in a name, any name will do, but
    • You are a good choice for the profile person.  
    • If your going to use data from 23andMe for the profile person, the profile name MUST match the 23andMe name.
  • Load a gedcom file for each profile if you have one.  If not just continue.
    • The gedcom file can be all of your relatives and more
    • Genome Mate will ask you for the name to associate with the profile person, and will strip out all but the profile person's direct ancestors.
    • The gedcom file format must be 5.5 in UTF8 format


Step 2:  Load 23andMe DNA Segments


Import Data Page

There are several methods for loading the DNA segment data for 23andMe profiles that can be mixed as needed.
529andYou:  The recommended method of importing 23andMe segment data is to use Neanderling's Chrome Plugin, 529andYou as it not only provides DNA segment data but triangulation and in common with (ICW) information as well. The Chrome browser is required.
  • Get Chrome Browser here
  • Get 529andYou here and be sure to click yes when asked to create a Chrome database.
  • Read about 529andYou here 
  • On 23andMe > My Results > Ancestry Tools > Family Inheritance: Advanced > Select any Compare profile > Compare > View in a Table > Click on 529 icon in upper right corner to open new tab 
  • On the 529andYou tab > Create 'To Do' Table > Highlight list of names > Copy & Paste into Notepad to use later
  • Click the button next to each Match name
  • Close the tabs that were open when they finish processing 
  • On the 23andMe tab  > Switch Profiles if there are more than one and repeat this step for each. 
  • Refresh the 529andYou tab or close then reopen through 23andMe
  • For each person in the Notepad list:  On the 529andYou tab > Display mode:  Profile and Overlapping Segment Links > Show matches of {name from Notepad list} > Create Match Table  [Note:  That the very first time it is faster to do this for each of your profile names rather than the Notepad list.]
  • Click on button next to a Profile person match
  • If available, Ctrl click on each link saying compare {name1} and {name2} to open FIA tabs for the comparison
  • Close new FIA tabs when finished processing
  • On the 529andYou tab > Create Match Table and repeat for next profile person on list
  • On the 529andYou tab >  Show matches of All > Download CSV 
  • In Genome Mate > Import Data > Select Data Source 23andMe > Load FIA Matches and ICW from 529andYou CSV file > Import Data from CSV File > Select file named 529andYou_{date}.csv
DNAGedcom:  This is the second preferred method of loading bulk DNA segments from 23andMe into Genome Mate.  It is the best method for loading Country of Ancestry DNA segments and also updates ICW data.
  • On DNAGedcom.com> 23andMe > Download 23andMe > Enter Email address > Enter 23andMe Password > Enter 23andMe Profile Name > Check Run FIA > Check Run AC > Check Run AF > Get Data and wait for it to finish processing 
  • This loads the shared matches:  In Genome Mate > Import Data > Select Match Data Source 23andMe > Load FIA Matches from DNAGedcom CSV file > Select file named {email name}_{profile name}_23andMe_FIA.csv 
  • This loads the Country of Ancestry (CoA) data:  In Genome Mate > Import Data > Select Data Source 23andMe > Load CoA Matches and ICWs from DNAGedcom > Select file named {email name}_23andMe_AF.csv
23andMe:  This is the least preferred method for loading DNA segments as it requires the data to be manually copied and pasted from the Family Inheritance: Advanced page into Genome Mate for up to 5 comparisons at a time.
  • On 23andMe > My Results > Ancestry Tools > Family Inheritance: Advanced > Select any Compare profile > Select up to 5 With Family Members > Compare > View in a Table > Select all (Ctrl A) > Copy (Ctrl C) 
  • In Genome Mate > Import Data > Select Data Source 23andMe> Copy/Paste Family Inheritance Advanced (FIA) > Follow directions
The following loads the 23andMe CoA file:
  • For each profile:  On 23andMe > My Results > Ancestry Tools > Countries of Ancestry > Show Results for:  {profile name} > At bottom of page Download {name} Countries of Ancestries Matches (CSV) 
  • For each profile:  In Genome Mate > Import Data > Select Data Source 23andMe > Load CoA Matches from 23andMe CSV file > Select profile name > Import Data from CSV File > Select file named ancestry_finder_{name}_{date}.csv


Step 3:  Load 23andMe Relative's Surnames

This step loads the Surnames for existing Relative records into Genome Mate.
  • For each 23andMe Profile:  In Genome Mate > Import Data > Select Data Source 23andMe> Load Relative Finder CSV file from 23andMe > Follow directions


Hints and Tips

  • There are two small arrows going in a circle to the left of your profile name. 
  • Left click to show overlapping segments.  Escape to return to the original screen.
  • Right click to bring up an overlapping segment dialog
  • Choose a Relative Name in the list of matches. 
  1. Choose a relative who matches you on more than one chromosome.
  2. Right click on it to show all matches
  3. Escape to return to the original screen.
  • Some Relatives will have a small symbol (Mark ICW segments) to the left of their name.   Hover (do not click) your mouse over the symbol. 
  • A series of colored bars will show you the relatives who are in common with the one you are hovering over. 
  • These people are related but not necessarily on the currently selected segment. 
  • Some ICW group symbols are in orange. 
  • The orange color means that the segment crosses a centromere, so the meaningful length is much shorter than the displayed length.   
  • If you hover over the symbol, it will show the length of the centromere. 

Backups & Restores 

The words of wisdom on creating backup files cannot be overemphasized.   Experimentation is encouraged, but make sure you have a safe harbor.


Donations

Genome Mate's continued development, support and enhancements on the internet are funded by your donations.  If you use the application, please consider making a donation through Paypal.

Copyright © Beckins LLC 2013-2014