GMP Performance

I know performance is a point of frustration with Genome Mate Pro (GMP) for some.  I can see a significant difference when loading data into my husband’s computer versus mine.

There is no doubt that GMP is much slower importing data than the old app. This is because the old app kept all data in memory and saved to disk every 5 minutes. Memory access is much faster than disk access but due to a Silverlight constraint, the in-memory database was limited in size.

The new app is virtually unlimited in size as it keeps the data in an SQLite database on disk.  However, the time it takes to load is a function of disk access speed and this varies from user to user.  I have been told that a solid state drive (SSD) is very efficient.

One way to improve performance without replacing your hardware is to set the import criteria in Options as highlighted below.  This will reduce the number of writes to the log file.

Starting with the 2016r01 release, it will be possible to enable in-memory journaling.  What this does is to write the SQLite journal file to memory rather than disk.  This is not recommended because there is a risk that if GMP is shutdown abnormally, the database may become corrupted and unusable.  If you do choose to use this option, BACKUP (File -> Backup) first.

~ Becky ~

P.S.  Tested loading data on my husband’s slow computer with these two options and the import time was amazing (197k records in less than 30 mins).

Import Issues?

Having issues importing data?  Data not there or rejected?  Formats occasionally change but most of the time the issue can be resolved by following these steps:

1. Verify that the data is not being hidden because of a filter selection on the Chromosome Browser page.  These should be set as above image to view all segments. 
2. Verify that the correct import option was selected.  There are many different import sources and sometimes multiple providers of the same data so ensure the import option reflects both the correct source and provider.
3. Verify that the data in question is contained in the import file and if using copy/paste that the data is copied from the Chrome browser.
4. Verify that the keys (name, kit, etc.) in the Profile record are entered correctly with the names and keys exactly as they are listed in the source data file.  Otherwise, the app will not be able to identify the correct profile.
5. Review the error generated in the log file.  Jim Sipe’s User Guide contains a list of error messages and possible resolutions. No log file? Verify that the log file is not open in another program such as Excel.
6. Verify that the settings are correct in Options -> App Settings

When the steps above have been verified and the issue is still not resolved then post the following screen shots on Facebook.  Be sure to include the version of the app and type of computer being utilized.

• Snip of the profile page in question
• Snip of the error in the log file
• Snip of the App Settings in Options
• Snip of GMP page (Relative, Chr Browser) showing problem

Please note that in options you can select Privatize the Display for Sharing before taking a screen shot.

If we cannot identify the issue from the screen shots, you may be asked to email your import file to me for further analysis on my test database.

~ Becky ~

Triangulation and ICW in Genome Mate Pro

The purpose of this post is to explain how triangulation and “in common with” (ICW) work in Genome Mate Pro.

Chromosome Browser

From the Chromosome Browser page, right click on a Relative to see what segments triangulate with that person and the profile person.

The first thing to note is that the app only displays what has been imported. It has no means to automatically identify either of these so if it is missing in the display then look to the import log to see if there is an error message associated with the import.

The second thing to note is that triangulation and ICW data are only retained for relatives found in the database. This is different from the old version of the app and it is important to load relative data before loading chromosome data.

Triangulation

In Genome Mate Pro, triangulation is based on two people being related to the profile person on the same chromosome segment so triangulation data has a chromosome number, base pair start and end points associated with it.

For example, profile person P matches relative A and matches relative B on the same segment (P==A, P==B). If relative A also matches relative B on the same segment (A==B) then P, A and B are triangulated. Otherwise, either A or B is likely related to profile person P on their maternal side while the other is related on their paternal side.

Data is loaded via various chromosome browser files such as the 529andYou and FTDNA Chromosome browser .csv files as well as specific triangulation imports such as GedMatch’s Tier 1 Triangulation.  Triangulations loaded from chromosome browser data have the import limitations listed on the Options page imposed on them as well.

Some caution should be exercised when a displayed triangulation is based on a very small segment overlap between the Relatives A and B as the endpoints from different sources tend to break at different intervals and endogamy can also cause havoc with the results.

In Common With (ICW)

ICW relatives do not have the chromosome, start point and end point data associated between them (typically from FTDNA) and as a result, the profile person P can have an ancestor in common with both relatives A and B but even if A and B have an ancestor in common, it is not necessarily the same one that is in common with profile person P.

Genome Mate Pro will display the people who are in common with the selected relative on the same segment.

Relative Page

Triangulation and ICW data are displayed on the Relatives page for the segment selected in the DNA Match Segments table on the left.  Since a Relative that triangulates with the selected person on that segment is already considered ICW, there may not be an ICW displayed in both the Triangulation and the ICW lists.

In summary, triangulation data has a segment specific information while ICW just says two people are related but gives no information on what segment that relationship occurs.

~ Becky ~

My Kirk Family

DNA evidence has been extremely useful in confirming my Kirk family as well as moving the family back several generations.

Lucinda Kirk

Lucinda Kirk was the wife of Henry Ridenour of Mercer Co. Missouri per my Aunt Blanche and mother of Thomas Riley Ridenour, my great grandfather.  The only census record for Lucinda and Henry can be found in the 1850 Mercer Co. Missouri census where they are listed with a daughter, Hester, age 2 indicating that they married about 1847.  In the 1860 census, Lucinda is missing but a 4 month old daughter, M.M. is enumerated indicating that she likely died in child birth in February of that year.  This is the only paper trail that I have found on Lucinda.

Because Lucinda named her son Thomas Riley, we suspected that Lucinda was a daughter to Thomas Riley Kirk.  In the 1840 Anderson Co. TN census, there were 2 females age 5 to 9 listed.  In 1850, there is only Nancy, age 15 and that would be consistent with Lucinda being the second daughter, married and living with Henry Ridenour in 1850.  This was confirmed by a strong DNA match with Wiley Clark Kirk’s grandson who is listed in Thomas Riley Kirk’s 1860 census as Clark, age 20.

Thomas Riley Kirk

Thomas was born 1790 in Virginia per most census records and his children’s birthplaces are listed as Tennessee.  There are two Kirk families in Tennessee, both with similar names.  In 1850, his wife is listed as Patsy and Martha in 1860.  Carrie Kirk lists her name as Martha Gwinn and their marriage as September 15, 1825 in Anderson Co. Tennessee. 

In 1998, Margaret Summitt sent me a transcript of the Kirk family history by Effie Lenore Kirk written about 1950 and based on bible records and family interviews.  In this, Thomas, John and Elijah are named as sons of John Kirk and that seems to be confirmed by census and land transactions in Anderson Co. Tennessee.  Effie was a descendant of John Kirk Jr. who married Eva Nausler while we descend through his brother, Thomas.

John Kirk

John purchased land in Anderson Co. Tennessee in 1807, witnessed by Elijah and sold land to John Kirk Jr. the same year.  In 1808, there is a Giles Co. Virginia land transaction from John Kirk of Anderson Co. Tennessee to an Isaiah Givens establishing that John’s family was in Giles Co. Virginia before coming to Tennessee.

Per “Kirk Families of Early Fauquier and Giles Counties” by Edgar C. Smith, there were two different Kirk families with similar names living in Giles Co. Virginia.  He references them as the Green Valley Kirks and the Stinking Creek Kirks.  Our Kirk line came from the latter as it was noted in the assessor’s records that John Kirk had moved to Anderson Co. Tennessee in 1807/08.

In 1801, Thomas Kirk of Montgomery Co. Virginia died naming as heirs 6 sons, 2 daughters and his wife Margot and a land grant to the same named heirs of Thomas Kirk, placed the acreage on Stinking Creek thus establishing Thomas and Margot Kirk as John’s parents.  Marriage records for these same children can be found in Montgomery Co. Virginia.

Thomas Kirk d. 1801

Thomas’ wife, Margot is named by others as the daughter of William Duncan and Ruth Rawley.  And while I have yet to search for the paper trail to confirm, I suspect that this is the source for the name Riley being passed down through the generations of our family even to one of my uncles.

Thomas is where my Kirk paper trail ends and the DNA investigation continues.

John Kirk d. 1730 Stafford Co. Virginia

John Kirk of Stafford Co. Virginia who married Francis Mason is thought to be the father of Thomas.  His wife who remarried William Clift and Joseph Kirk “eldest son” of Orange Co. North Carolina are named in land transactions.  From Max Kirk on Gedforum:

1757 June 15. Frances Clift of Culpeper County, widow, to George Roberts of
same, planter. For L100 current money. 400 acres which was granted to Joseph
Cooper by patent 24 June 1726 and by deeds of lease and release 2-3 Oct. 1727
recorded in the County Court of Spottsylvania was conveyed by Joseph Cooper to
John Kirk of Overwharton Parish, Stafford County, who was then husband of said
Frances Clift, and 11 Feb. 1728/29 John Kirk did make his last will and testament
whereby he among other things bequeathed to his wife Frances all his lands, and
his will was recorded in the County Court of Stafford 8 July 1730. Frances after
the death of her husband intermarried with William Clift who is since dead...
Witnesses: Wm. Green, Thos. Slaughter, John Field.

1757 Apr 22. Bond of Joseph Kirk of Orange Co. N.C., to George Roberts of
Culpeper County. George Roberts hath agreed to purchase of Mrs. Frances Clift
400 acres whereon Frances Clift now liveth which was bequeathed to Frances Clift
by John Kirk her former husband... Joseph Kirk being eldest son and heir at law
as well of John Kirk, deceased, as of Frances Clift, and being satisfied that it was
the design of his deceased father that his mother should enjoy the 400 acres
forever... Joseph Kirk nor his heirs shall not demand the 400 acres. Witnesses:
Adam Menzies, James Slaughter, William Kirtley.

1768 Sept 5/6. George Roberts and Elizabeth his wife of Culpeper County to
Joseph Burt of Cumberland County, Pa., and William Green of Culpeper
County... 184 acres in St. Mark's Parish... on the bank of Mountain Run by the
mouth of a gully... in an island of Thorney Branch standing among rocks... part of
a tract containing 400 acres which was granted by patent to Thomas Cooper 24
June 1726 and by Cooper sold to John Kirk who died thereof seized and by his last
will and testament bequeathed the same to Francs his wife...Witnesses: Benja.
Roberts, Wm. Delany, Joseph Roberts.

I have several maternal DNA matches with descendants of the Mason family of Stafford Co. Virginia but yet to find any evidence confirming this relationship.  However, I do have two separate DNA triangulations indicating that our family is descended from John’s parents, Christopher Kirk and Ann Wright.

Christopher Kirk d. 1721

There are two separate DNA triangulation's to indicate that Christopher Kirk and Ann Wright were the grandparents of Thomas Kirk d. 1801 Montgomery Co. Virginia.

Kirk MRCA	Chromosome 5	Chromosome 19
Lucinda Kirk d.1850 Mercer MO	Carrie Nelson's  grandchildren	Uncle Ray
Thomas Riley Kirk d.1882 Mercer MO	Clark Kirk's  grandson
John Kirk  d.1850 Anderson TN
Thomas Kirk d.1801 Montgomery VA
Christopher Kirk d.1821 Lancaster VA	C. Jones	W.H.Mitchell & D. Akins
Christopher Kirk d.1705 Northampton VA		M. Abrams

Summary

DNA testing has not only confirmed family testimony about the Kirk line but has aided in moving the ancestral line back to the immigrant, Christopher.  We are also fortunate in being able to identify the Kirk haplogroup as R-P312 from one of his direct ancestors.

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

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

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