Introducing the Match-Maker-Breaker Tool for Parental Phasing

A few days after I published the article, Concepts – Segment Size, Legitimate and False Matches, Philip Gammon, a statistician who lives in Australia, posted a comment to my blog.

Great post Roberta! I’m a statistician so my eyes light up as soon as I see numbers. That table you have produced showing by segment length the percentage that are IBD is one of the most useful pieces of information that I have seen. Two days to do the analysis!!! I’m sure that I could write a formula that would identify the IBD segments and considerably reduce this time.

By this time, my eyes were lighting up too, because the work for the original article had taken me two days to complete manually, just using segments 3 cM and above. Using smaller segments would have taken days longer. By manually, I mean comparing the child’s matches with that of both parents’ matches to see which, if either, parent the child’s match also matches on the same segment.

In the simplest terms, the Segment Size article explained how to copy the child’s and both parents’ matches to a spreadsheet and then manually compare the child’s matches to those of the parents. In the example above, you can see that both the child and the mother have matches to Cecelia. As it turns out, the exact same segment of DNA was passed in its entirety to the child from the mother, who is shown in pink – so Cecelia matches both the child and the parent on exactly the same segment.

That’s not always the case, and the Segment Size article went into much greater detail.

For the past month or so, Philip and I have been working back and forth, along with some kind volunteers who tested Philip’s new tool, in order to create something so that you too can do this comparison and in much less than two days.

Foundation

Here’s the underlying principle for this tool – if a child has a match that does NOT match either parent on the same segment, then the match is not a legitimate match. It’s a false match, identical by chance, and it is NOT genealogically relevant.

If the child’s match also matches either parent on the same segment, it is most likely a match by descent and is genealogically relevant.

For those of you who noticed the words “most likely,” yes, it is possible for someone to match a parent and child both and still not phase (or match) to the next higher generation, but it’s unusual and so far, only found in smaller segments. I wrote about multiple generation phasing in the article, “Concepts – Segment Survival – 3 and 4 Generation Phasing.” Once a segment phases, it tends to continue phasing, especially with segments above about 3.5 cM.

For those who have both parents available to test, phased matching is a HUGE benefit.

But I Have Only One Parent Available

You can still use the tool to identify matches to that one parent, but you CANNOT presume that matches that DON’T match that parent are from the other (missing) parent. Matches matching the child but not matching the tested parent can be due to:

• A match to the missing parent
• A false match that is not genealogically relevant

According to the statistics generated from Philip’s Match-Maker-Breaker tool, shown below, segments 9 cM and above tend to match one or the other parent 90% or more of the time.  Segments 12 cM and over match 97% of the time or more, so, in general, one could “assume” (dangerous word, I know) that segments of this size that don’t match to the tested parent would match to the other parent if the other parent was available. You can also see that the reliability of that assumption drops rapidly as the segment sizes get smaller.

Platform

This tool was written utilizing Microsoft Excel and only works reliably on that platform.

If you are using Excel and are NOT attempting to use MAC Numbers, skip this section.  If you want to attempt to use Numbers, read this section.

I tried, along with a MAC person, to try to coax Numbers (free MAC spreadsheet) into working. If you have any other option other than using Numbers, so do. Microsoft Excel for MAC seemed to work fine, but it was only tested on one MAC.

Here’s what I discovered when trying to make Numbers work:

• You must first launch numbers and then select the various spreadsheets.
• The tabs are not at the bottom and are instead at the top without color.
• The instructions for copying the formulas in cells H2-K2 throughout the spreadsheet must be done manually with a copy/paste.
• After the above step, the calculations literally took a couple hours (MacBook Air) instead of a couple minutes on the PC platform. The older MAC desktop still took significantly longer than on a Microsoft PC, but less time than the solid state MacBook Air.
• After the calculations complete, the rows on the child’s spreadsheet are not colored, which is one of the major features of the Match-Maker-Breaker tool, as Numbers reports that “Conditional highlighting rules using formulas are not supported and were removed.”
• Surprisingly, the statistical Reports page seems to function correctly.

How Long Does Running Match-Maker-Breaker Tool on a PC Take?

The first time I ran this tool, which included reading Philip’s instructions for the first time, the entire process took me about 10 minutes after I downloaded the files from Family Tree DNA.

Vendors

Transfer Kits

It’s strongly suggested that all 3 individuals being compared have tested at Family Tree DNA or on the same chip version imported into Family Tree DNA.

Matches not run on the same chip as Family Tree DNA testers can only provide a portion of the matches that the same person’s results run on the FTDNA chip can provide. You can run the matching tool with transferred results, but the results will only provide a subset of the results that will be provided by having all parties that are being compared, meaning the child and both parents, test at Family Tree DNA.

The following products versions CAN be all be compared successfully at Family Tree DNA, as they all utilize the same Illumina chip:

• All Family Finder tests
• Ancestry V1 (before May 2016)
• 23andMe V3 (before November 2013)
• MyHeritage

The following tests do NOT utilize the same Illumina testing platform and cannot be compared successfully with Family Finder tests from Family Tree DNA, or the list above. Cross platform testing results cannot be reliably compared. Those that DO match will be accurate, but many will not match that would match if all 3 testers were utilizing the same platform, therefore leading you to inaccurate conclusions.

• Ancestry V2 (beginning in May 2016 to present)
• 23andMe V4 (beginning November 2013 to present)

The child and two parents should not be compared utilizing mixed platforms – meaning, for example, that the child should not have been tested at FTDNA and the parents transferred from Ancestry on the V2 platform since May 2016.

If any of the three family members, being the child or either parent, have tested on an incompatible platform, they should retest at Family Tree DNA before using this tool.

What You Need

• You will need to download the chromosome match lists from the child and both parents, AT THE SAME TIME. I can’t stress this enough, because any matches that have been added for either of the three people at a later time than the others will skew the matching and the statistics. Matches are being added all the time.
• You will also need a relatively current version of Excel on your computer to run this tool. No, I did not do version compatibility testing so I don’t know how old is too old. I am running MSOffice 2013.
• You will need to know how to copy and paste data from and to a spreadsheet.

To download your matches, sign on to each account. On your main page, you will see the Family Finder section, and the Chromosome Browser. Click on that link.

At the top of the chromosome browser page, below, you’ll see the image of chromosomes 1 through X. At the top right, you’ll see the option to “Download all matches to Excel (CSV Format). Click on that link.

Next, you’ll receive a prompt to open or save the file. Save it to a file name that includes the name of the person plus the date you did the download. I created a separate folder so there would be no confusion about which files are which and whether or not they are current.

Your match file includes all of your matches and the chromosome matching locations like the example shown below.

These files of matches are what you’ll need to copy into the Match-Maker-Breaker spreadsheet.

Do not delete any information from your match spreadsheets. If you normally delete small segments, don’t. You may cause a non-match situation if the parent carries a larger portion of the same segment.

You can rerun the Match-Maker-Breaker tool at will, and it only takes a very few minutes.

The Match-Maker-Breaker Tool

The Match-Maker-Breaker Tool has 5 sheets when you open the spreadsheet:

• Results – The page where your statistical results will be placed.
• Child – The page where you will paste the child’s matches and then look at the match results after processing.
• Father – The page where you will paste the father’s matches.
• Mother – The page where you will paste the mother’s matches.

Make a Copy

After you download the tool, make a copy on your system. You’ll want to save the Match-Maker-Breaker spreadsheet file for each trio of people individually, and you’ll want a fresh Match-Maker-Breaker spreadsheet copy to run with each new set of download files.

Instructions

I’m not going to repeat Philip’s instructions here, but please read them entirely before beginning and please follow them exactly. Philip has included graphic illustrations of each step to the right of the instruction box. The spreadsheet opens to the Instructions page. You can print the instruction page as well.

Copy/Pasting Data

When copying the parents’ and child’s data into the spreadsheets, do NOT copy and paste the entire page by selecting the page. Select and copy the relevant columns by highlighting columns A through G by touching your cursor to the A-G across the top, as shown below.  After they are selected, then click on “copy.” In the child’s chromosome browser download spreadsheet, position the curser in the first cell in row 1 in the child’s page of the Match-Maker-Breaker spreadsheet and click on “paste.”

Do NOT select columns H-K when highlighting and copying, or your paste will wipe out Philip’s formulas to do calculations on the child’s tab on the spreadsheet.

The example above, assuming that Annie is the last entry on the spreadsheet, shows that I’ve highlighted all of the cells in columns A-G, prior to executing the copy command. Your spreadsheets of course will be much longer.

I wrote a very quick and dirty article about using Excel here

The Match Making Breaking Part

After you copy the formulas from rows H2 to K2 through the rest of the spreadsheet by following Philip’s instructions, you’ll see the results populating in the status bar at the bottom. You’ll also see colors being added to the matches on the left hand side of the spreadsheet page and counts accruing in the 4 right columns. Be patient and wait. It may take a few minutes. When it’s finished, you can verify by scrolling to the last row on the child’s page and you’ll see something like the example below, where every row has been assigned a color and every match that matches the child and the father, mother, both or is found in the HLA region is counted as 1 in the right 4 columns.

In this example, 5 segments, shown in grey, don’t match anyone, one, shown in tan is found in the HLA region, and three match the father, in blue.

Output

After you run the Match-Maker-Breaker tool, the child’s matches on the Child tab will be identified as follows:

This means that segment of the child that matches that individual also matches the father, the mother, both parents, the HLA region, or none of the above on all or part of that same segment.

What is a Match?

Philip and I worked to answer the question, “what is a match?” In the Concepts article, I discussed the various kinds of matches.

• Full match: The child’s match and parent’s match share the same exact segment, meaning same start and end points and same number of SNPs within that segment.
• Partial match: The child’s match matches a portion of the segment from the parent – meaning that the child inherited part of the segment, but not the entire segment.
• Overhanging match: The child’s match matches part or all of the parent’s segment, but either the beginning or end extends further than the parents match. This means that the overlapping portion is legitimate, meaning identical by descent (IBD), but the overhanging portion is identical by chance (IBC.)
• Nested match: The child’s match is smaller than the match to the parent, but fully within the parent’s match, indicating a legitimate match.
• No match: The person matches the child, but neither parent, meaning that this match is not legitimate. It’s identical by chance (IBC).

Full matches and no matches are easy.

However, partial matches, overlapping matches and nested matches are not as straightforward.

What, exactly, is a match? Let’s look at some different scenarios.

If someone matches a parent on a large segment, say 20cM, and only matches the child on 2cM, fully within the parent’s segment, is this match genealogically relevant, or could the match be matching the child by chance on a part of the same segment that they match the parents by descent? We have no way to know for sure, just utilizing this tool. Hopefully, in this case, the fact that the person matches the parent on a large segment would answer any genealogical questions through triangulation.

If the person matches the parent but only matches the child on a small portion of the same segment plus an overhanging region, is that a valid match? Because they do match on an overhanging region, we know that match is partly identical by chance, but is the entire match IBC or is the overlapping part legitimate? We don’t know. Partly, how strongly I would consider this a valid match would be the size of the matching portion of the segment.

One of the purposes of phasing and then looking at matches is to, hopefully, learn more about which matches are legitimate, which are not, and predictors of false versus legitimate matches.

Relative to this tool, no editing has been done, meaning that matches are presented exactly as that, regardless of their size or the type of match. A match is a match if any portion of the match’s DNA to the child overlaps any portion of either or both parent’s DNA, with the exception of part of chromosome 6. It’s up to you, as the genealogist, to figure out by utilizing triangulation and other tools whether the match is relevant or not to your genealogy.

If you are not familiar with identical by descent (meaning a legitimate match), identical by population (IBP) meaning identical by descent but because the population as a whole carries that segment and identical by chance (IBC) meaning a false match, the article Identical by…Descent, State, Population and Chance explains the terms and the concepts so that you can apply them usefully.

After analyzing the results of several people, the area of chromosome 6 that includes the HLA region has been excluded from the analysis. Long known to be a pileup region where people carry significant segments of the same DNA that is not genealogically relevant (meaning IBP or identical by population,) this region has found to be often unreliable genealogically, and falls outside the norm as compared to the rest of the segments. This area has been annotated separately and excluded from match results. This was the only region found to universally have this effect.

This does not mean that a match in this region is positively invalid or false, but matches in the HLA region should be viewed very skeptically.

The Results Tab – Statistics

Now that you’ve populated the spreadsheet and you can see on the Child tab which matches also match either or both parents, or neither, or the HLA region, go to the Results tab of the spreadsheet.

This tab gives you some very interesting statistics.

First, you’ll see the number and percent of matches by chromosome.

The person compared was a female, so she would have X matches to both parents. However, notice that X matching is significantly lower than any of the other chromosomes.

Frankly, I’ve suspected for a long time that there was a dramatic difference in matching with the X chromosome, and wrote about it here. It was suggested by some at the time that I was only reporting my personal observations that would not hold beyond a few results (ascertainment bias), but this proves that there is something different about X chromosome matching. I don’t know what or why, but according to this data that is consistent between all of the beta testers, matching to the X chromosome is much less reliable.

The second statistics box you will see are statistics for the matches to the child that also match the parents. The actual matches of the child to the parents are shown as the 23 shown under “excluded from calculations.”

The next group of statistics on your page will be your own, but for this example, Philip has combined the results from several beta testers and provided summary information, so that the statistics are not skewed by any one individual.

Next, the match results by segment size for chromosomes 1-22. Philip has separated out segments with less than 500 SNPs and reports them separately.

You will note that 90% or more of the segments 9 cM and above match one of the two parents, and 97% or more of segments 12cM or above.

The X chromosome follows, analyzed separately. You’ll notice that while 27% of the matches on chromosomes 1-22 match one or both parents, only 14% of the X matches do.

Even with larger segments, not all X segments match both the child and the parents, suggesting that skepticism is warranted when evaluating X chromosome matches.

Philip then calculated a nice graph for showing matching autosomal segments by cM size, excluding the X.

The next set of charts shows matches by SNP density. Many people neglect SNP count when evaluating results, but the higher the SNP count, the more robust the match.

Note that SNP density above 2,200 almost always matched, but not always, while SNP density of 2,800 reaches the 97% threshold..

The X chromosome, by SNP count, below.

X segment reach the 100% threshold about 1600, however, we really need more results to be predictive at the same level as the results for chromosomes 1-22.  Two data samples really isn’t adequate.

Once again, Philip prepared a nice chart showing percentage of matching segments by SNP count, below.

Predictive

In the Segment Survival – 3 and 4 Generation Phasing article, one can see that phased matches are predictive, meaning that a child/parent match is highly suggestive that the segment is a valid segment match and that it will hold in generations further upstream.

Several years ago, Dr. Tim Janzen, one of the early phasing pioneers, suggested that people test their children, even if both parents had already tested. For the life of me, I couldn’t understand how that would be the least bit productive, genealogically, since people were more likely to match the parents than the children, and children only carry a subset of their parent’s DNA.

However, the predictive nature of a segment being legitimate with a child/parent match to a third party means that even in situations where your own parent isn’t available, a match by a third party on the same segment with your child suggests that the match is legitimate, not IBC.

In the article, I showed both 3 and 4 generations of phased comparisons between generations of the same family and a known cousin. The results of the 5 different family comparisons are shown below, where the red segments did not phase or lost phasing between generations, and the green segments did phase through multiple generations.

Very, very few segments lost phasing in upper (older) generations after matching between a parent and a child. In the five 4-generation examples above, only a total of 7 groups of segments lost phasing. The largest segment that lost phasing in upper generations was 3.69 cM. In two examples, no segments were lost due to not phasing in upper generations.

The net-net of this is that you can benefit by testing your children if your parents aren’t available, because the matches on the segment to both you and the child are most likely to be legitimate. Of course, there will be segments where someone matches you and not your child, because your child did not inherit that segment of your DNA, and those may be legitimate matches as well. However, the segments where you and your child both match the same person will likely be legitimate matches, especially over about 3.5 cM. Please read the Segment Survival article for more details.

If you want to order additional Family Finder tests for more family members, you can click here.

Group Analysis

Philip has performed a group analysis which has produced some expected results along with some surprising revelations. I’d prefer to let people get their feet wet with this tool and the results it provides before publishing the results, with one exception.

In case you’re wondering if the comparisons used as examples, above, are representative of typical results, Philip analyzed 10 of our beta testers and says the following:

The results are remarkably consistent between all 10 participants. Summing it up in words: with each person that you match you will have an average of 11 matching segments. Three will be genuine and will add to [a total of] 21 cM. Eight will be false and add to [a total of] 19 cM.

Philip compiled the following chart summarizing 10 beta testers’ results. Please note that you can click to enlarge the images.

The X, being far less consistent, is shown below.

We Still Need Endogamous Parent-Child Trios

When I asked for volunteer testers, we were not able to obtain a trio of fully endogamous individuals. Specifically, we would like to see how the statistics for groups of non-endogamous individuals compare to the statistics for endogamous individuals.

Endogamous groups include people who are 100% Jewish, Amish, Mennonite, or have a significant amount of first or second cousin marriages in recent generations.

Of these, Jewish families prove to be the most highly endogamous, so if you are Jewish and have both Jewish parents’ DNA results, please run this tool and send either Philip or me the resulting spreadsheet. Your results won’t be personally identified, only the statistics used in conjunction with others, similar to the group analysis shown above. Your results will be entirely anonymous.

Philip’s e-mail is philip.gammon@optusnet.com.au and you can reach me at roberta@dnaexplain.com.

Caveat

Philip has created the Match-Maker-Breaker tool which is free to everyone. He has included some wonderful diagnostics, but Philip is not providing individual support for the tooI. In other words, this is a “what you see is what you get” gift.

Thank You and Acknowledgements

Of course, a very big thank you to Philip for creating this tool, and also to people who volunteered as alpha and beta testers and provided feedback. Also thanks to Jim Kvochick for trying to coax Numbers into working.

Match-Maker-Breaker Author Bio:

I asked Philip to describe himself.

I’d describe myself as a business analyst with a statistics degree plus an enthusiastic genetic genealogist with an interest in the mathematical and statistical aspects of inheritance and cousinship.

The important aspect of Philip’s resume is that he is applying his skills to genetic genealogy where they can benefit everyone. Thank you so much Philip.

Watch for some upcoming guest articles from Philip.

______________________________________________________________

Disclosure

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Thank you so much.

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26 thoughts on “Introducing the Match-Maker-Breaker Tool for Parental Phasing”

1. Thanks! I believe I’ve followed instructions, but some of the result tables are blank and it says “problem” in cells M18,M19,N18 and N19 on the result tab (the rest says “OK”). Any idea why that might be?

• Hi, I haven’t seen that problem myself and can’t think what would be causing it. From the other comments I can’t see that anyone else has encountered this issue. Could you give it another try? Philip

2. Hi Roberta and Philip,

Thanks for a great tool. I actually got a higher % of segment matches with the X but this may be due to a low sample size.

Size (centiMorgans) Matching Segments Parent/Child Matches Percentage Matches
1 – 1.99 4 4 100%
2 – 2.99 11 3 27%
3 – 3.99 8 3 38%
4 – 4.99 3 2 67%
5 – 5.99 0 0
6 – 6.99 0 0
7 – 7.99 0 0
8 – 8.99 0 0
9 – 9.99 0 0
10 – 10.99 0 0
11 – 11.99 0 0
12 – 12.99 0 0
13 – 13.99 0 0
14 – 14.99 0 0
15 – 15.99 0 0
16 – 16.99 0 0
17 – 17.99 0 0
18 – 18.99 0 0
19 + 0 0
Sub-total 26 12 46%
Segments with < 500 SNPs 0 0
Total 26 12 46%

Best Wishes

Gareth

• Hi Gareth,
You’re right, the sample size is too small to draw any meaningful conclusions. Even the combined results from 10 participants didn’t contain enough matching segments on the X chromosome to really determine the shape of the curve. But I have observed that the number of SNPs a segment contains is a more reliable indicator of its likelihood to be a genuine IBD segment. The cM is just a measure of how likely the segment is to be divided by a crossover in meiosis but it’s the comparison between two people of their SNP values that determines whether a segment is a match or not. There’s seems to be a lower sampling rate of SNPs tested on the X chromosome. In rough numbers there is an average of about 200 SNPs per cM on the autosomes but only about half that on the X. Therefore, as a rough guide an X segment is about as likely to be genuinely IBD as an autosomal segment of about half its length. So to be more than 90% confident that an X segment is IBD it would need to be longer than 20 cM.
Philip

3. Fascinating! It’s becoming a truism in my never ending quest to learn about this DNA business that someone will come along and figure out a tool to quickly do what I’ve been doing by hand. I keep a combined spread sheet of all segments for my parents and myself that identifies matching segments. It is appended as new matches come along and is now up to 89000 plus rows. In creating it I have observed much of what the statistics verify, such as for common person matches most of the smallest segments do not match but at at least one of the longest ones invariably does. It is nice to generate and review the charts that actually show this. By the way, my autosomal and X came out the same at 26%. I suspect my mom’s X is pushing it higher than expected as she is X blessed with person matches (747 of 2826) who have yielded over 1000 matching segments. This is twice my X numbers; I am female with a slightly smaller person match total than Mom. Dad’s X matches are 104/2384 with 109 segments.

4. This was fascinating! My X matches were at 8%. Included in those matches is, though, is my sister and brother, and a 1st cousin (child of my mom’s sister). So, my numbers are actually skewing higher because of close kin also tested. My sister’s X matches were at 9%. My brother’s were at 44% (but of the 7 segments where he matched a parent, 4 were shared by my sister and me. He and our 1st cousin don’t share any X at all, although it was technically possible they could have. All of our matches with parents, though, were = 13 cM were matches w/ parents. Useful to know — and to focus on.

Thank you, thank you, Philip and Roberta!!

5. I’m having issues similar to Armund, the first person to reply.

The 2 things I am unsure of are:

1. The directions say paste into cell A1, but the pictures show the headers in A1 and the pasted data starting in A2. Which is correct, the text or the pictures? Perhaps this is my problem, since I chose to follow the pictures and pasted beginning in A2. I’ll probably try for a third time with that change–maybe the third time is the charm 🙂
2. I’m not sure where I’m supposed to click to trigger the auto-fill function in Step 4, when pasting the formulas from H to K in all rows with data. It takes forever to highlight all the child rows to paste into. Any chance you could and a screenshot of the little square I’m supposed to click? Is this perhaps this is a PC feature or something in a newer version of Excel?

What I see:
In the Child tab, columns H & I, there are errors that the formulas refer to empty cells. There is no summary table at the end of the data as described in the post by Roberta.

In the results tab, my name shows up after the “Summary Statistics for:” as expected. But, my father’s name in the table below this is replaced by “#Ref!” and the cell is protected so not showing me the problem. There are no matches with my mother and 7 matches with both parents. I have “problem” in cells L18,19, 22, 23 and N 18-21

I’ve pasted the table below, a little hard to read with the wrapping, but it may point out the problem. I’ve changed mom’s name to “Mother”

My suspicion is the calculations in the Child tab may not have completed correctly. Is there a way to trigger it to recalculate all the formulas? I can try shutting everything else down to boost the memory available.

The other issue may be that I’m on an older MacBook Pro (2011) and though I am using Excel, it is the 2008 version for the Mac.

Here is the results table with data, the other results tables are all blank, reinforcing my suspicion that the calculations did not complete correctly.

Chromosome Matching Segments Parent/Child Matches Father/Child Matches Mother/Child Matches Matches with Both Parents “Non-
Matches”
Autosomal 0 3480 3487 0 7 0
X Chromo 0 6 6 0 0 0
Sub-total 0 3486 3493 0 7 0

Excluded from calculations:
#REF! 0 0 0 0
Mother 23 0 0 23
HLA region 0 202 162 41 1 0
Sub-total 23 202 162 41 1 23
Grand Total 23 3688 3655 41 8 23

I know this is an “as is” tool, but if anyone sees what I’m doing wrong, please let me know. This looks like a great tool and I’m eager to put it to use!

Thanks!

• Both were correct for what they said. On was without headers and one is with headers. I have replaced the verbiage with a new photo to avoid confusion. Please take a look again for paste instructions. The goal is to not wind up with two header rows and not to overwrite the formula columns in the spreadsheet.

Regarding the little X box at the bottom right corner of H2-K2 when you highlight them, it’s present in Excel on PCs and not present in Numbers. I can’t speak for Excel on the Mac, but if it’s not there, just highlight those 4 cells and pull the highlighted columns to the bottom of the spreadsheet. It shouldn’t take long.

• Hi Roberta,
I was careful to not overwrite the child columns H2-K2 and the formulas the contained and I only copied the data to leave the header filters in place. The “X box” may be present in a later version for Excel for Mac, I’m not seeing it under the 4 cells I highlight in the first row of H2-K2. I have been dragging it down to the bottom, but it takes a while with that many rows, and a slower machine.

I think my problem is the memory available in my older Mac Book Pro, it might not have had enough to process it. I was getting most of my Dad’s and a little of my Mom’s matches processed.

I eventually got the results table with Results tab checks showing “OK,” and it looks like it worked, I’ve been spot checking the matches and everything seems there.

I’m going to have to increase the memory and see if the performance improves. I know patience is a virtue, but it is one I don’t have 🙂

Using Philip’s filters on the headers allow me to sort easily and see all the overlapping matches and also see which matches I shared with my parents.

I now have to convince my cousins to test so I can do the same with my parent’s siblings matches! I’ve been telling everyone children didn’t need to test if their parents did! 🙂

Many thanks for your ongoing instruction and help Roberta! I’m always pointing new people here to learn. HUGE thanks to both you and Philip for the very cool new tool! You two make a great team!

Elle

PS. Is there any way we can tell if someone transferred their data from Ancestry or 23&me? In the chromosome browser it says an orange asterisk indicates a 3rd party match, and allows you to hide them with a check box. I assumed 3rd party meant transfer. I haven’t seen an asterisk, and I have a close match that is a recent transfer from Ancestry, so it doesn’t seem to be working or my assumption about what 3rd party means is wrong.

• I’m not sure if or how to tell if someone is a transfer. For parent child, you’ll know, because you’ll know as you’ll be controlling the kits. As for others, I think that indicator is supposed to work, but I don’t think that it is.

• Elle, I’m glad that you got it working!

Like Roberta, I don’t see any indication on FTDNA if a match is from a transfer kit. But I think that I know how to identify some of them. If you have any matching segments that contain less than 500 SNPs – it’s a transfer kit. You can use the filters in column G on the Match-Maker-Breaker to find these.

Segments with less than 500 SNPs only started appearing in matching segment files after FTDNA started accepting V4 transfers from 23andMe and V2 transfers from AncestryDNA in February of this year. I think that transfers from older tests (23andMe V3 and AncestryDNA V1) will have all matching segments containing more than 500 SNPs so you won’t be able to use this method to find those ones.

6. Roberta,

*Three* of my brothers match someone in a “Pile-Up” region on chromosome 15; segments 23.9 – 29.1. Is it more likely this is IBD as opposed to IBP.

Thanks, Robin

On Thu, Apr 6, 2017 at 6:29 PM, DNAeXplained – Genetic Genealogy wrote:

> robertajestes posted: “A few days after I published the article, Concepts > – Segment Size, Legitimate and False Matches, Philip Gammon, a statistician > who lives in Australia, posted a comment to my blog. Great post Roberta! > I’m a statistician so my eyes light up as soon as I se” >

• Part of the answer would depend on the size. Your brothers obviously inherited the same DNA from both your parents on that segment. The fact that all 3 match doesn’t make it more likely to be IBD. Now if you’re matching cousins on that same segment to, then yes.

7. Hi Roberta,
thank you for great article and tool.
It looks it should work for 23andMe matches too, but I’m not sure. For one person and his parents the results looks good:
http://i68.tinypic.com/2146tyb.png

but for the second person and her parents not.
http://i68.tinypic.com/30v21a9.png

Mother of the second person has 80% Ashkenazi origin and much more matches.
This second person and her parents have Family Finder test on FTDNA as well, but I’m not able to download Chromosome_Browser_Results for any person with Ashkenazi origin (I manage 4), while download for other persons I manage works fine. I already reported the problem to FTDNA. If it will be working I will compare the results.
Petr

• The problem with 23andMe is that there is no way to know if the people matching either of the three people, meaning, child and both parents, have authorized sharing for the other two. Unless all people have authorized sharing, the matches won’t be the same because some people who would match both are only authorized to match one.

• Thank you for the upcoming Ashkenazi comparison.

• Finally I was able to download the files files from FTDNA website, but it was necessary to try it 20 times. Here is the result for the same 2nd person, she has 60015 segment matches, her father 3784 segment matches, her mother 171710 segment matches. Calculation took about 20 minutes on 8 core 3.4 GHz Processor!
http://i64.tinypic.com/118n0w7.png

8. Thanks for you hard work, both of you, I didn’t had time to do it manually. I’ll give it a try in a few weeks, when things will finally wind down. Hopefully.

9. So this sounds like a great tool! Would there be any use in using it with my dad and his aunt who tested? His parents, of course, are long gone. Matches that don’t match his aunt might still be valid – but if they DO, then I’d know for sure they were valid maternal side matches, right?

My mother was never tested, but i definitely need to run this with my dad for both my sister and me.

• The statistics will be irrelevant, but it will still tell you who matches whom, so I think it would be valuable in that way.

10. I don’t have both parents but I have my mother’s sister. If I used her as my mother, I think I’ll still have matches that don’t match me and my father but are not necessarily matching my real mother, that is, are IBC *OR* don’t match my maternal aunt but would match my mother if her DNA was available, right?

• Yes, that’s correct.