Dear Jim, This gets a little tricky. All "shared segments" appear as HIRs in 23andMe and FF comparisons. However, not all HIRs are "shared segments" in the strict sense of the word. I would prefer to think of HIRs that are IBD as being "shared segments". The term "shared segment" suggests that there is a common ancestor involved who contributed the "shared segment". However, some HIRs don't involve a common ancestor between the people who share those HIRs. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett Sent: Saturday, October 19, 2013 8:21 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them I thought an HIR was the same thing as a shared segment, because a shared segment has the same definition as Tim's HIR. Jim - Sent from my iPhone - FaceTime!

I agree with Tim, the Net doesn't have a good definition of HIR. Here's a few definitions online: FTDNA: A half identical region (HIR) is when two people's share a DNA segment that half matches. The half identical region may be either identical by descent (IBD) or identical by state (IBS). 23andMe Family Traits: Genome View shows which parts of two related people's genomes appear to be inherited from a common ancestor. In reality, the genome is organized into 22 pairs of chromosomes, plus the sex chromosomes (two X, or one X and one Y). We show only one chromosome out of each pair, but we color them to show whether one copy is identical (i.e. half-identical), or both copies are identical (i.e. completely identical) between two people. DNA Testing and Genealogy (http://www.johnbrobb.com/JBRdna.htm) half-identical said of two humans who share at least one allele value at a particular SNP. Long consecutive stretches of half-identical sampled SNPs, measured in CM's (centimorgans, which adjust for the variant rates of crossover in different chromosomes) are indicative of a shared descent from a common ancestor. The term HIR is sometimes used to mean half-identical region, whose length may be quantified either in cMs or in the number of SNPs. The principle testing companies at present, 23andME, and FTDNA, consider anywhere from 5-7 cMs (or about 500-700 SNPs) to be the minimum length to be possibly indicative of a reasonably close cousin relationship. E -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett Sent: Saturday, October 19, 2013 8:21 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them I thought an HIR was the same thing as a shared segment, because a shared segment has the same definition as Tom's HIR. Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 10:59 PM, "Tim Janzen" <tjanzen@comcast.net> wrote: > Dear Karen, > HIR stands for half-identical region. It is an extremely important > term for genetic genealogists interested in autosomal DNA to > understand well. Because I couldn't find a good definition for an HIR > 9 months or so ago, I wrote my own. It is as follows: > > Half-identical region: a region of two paired chromosomes where at > least one of the two alleles from one person's pair of chromosomes > matches at least one of the two alleles from a different person's pair > of chromosomes throughout the entire region. A half-identical region > may be either identical by descent (IBD) or identical by state (IBS). > > Some scientists use IBS to mean an HIR. I think things are simpler > and clearer if you use the term HIR in the right context and use IBS > only for HIRs that are false matches (not the result of a shared > common ancestor for the HIR in question). This topic came up on the > RootsWeb DNA list in 2009 shortly after 23andMe released Relative > Finder. Ann Turner's comments at > http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2009-11/12 > 572588 > 09 are instructive. > Sincerely, > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges > Sent: Saturday, October 19, 2013 2:29 PM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of > them > > What is HIR short for please? > > Karen ______________________________ For answers to Frequently Asked Questions about mailing lists, please see: http://dgmweb.net/MailingListFAQs.html ------------------------------- To unsubscribe from the list, please send an email to AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Hi Tim Your answer was exactly what I needed to know. I thought it couldn't be so amazing [the new tools although they are wonderful] and your mention of endogamous populations explains the why of how you can match the same people as a known relative but it can still be by coincidence and not related. So the only confident matches for that line are those in the same location as my cousin that we both have in common. Thanks very much Tim Karen On Sat, Oct 19, 2013 at 5:19 PM, Tim Janzen <tjanzen@comcast.net> wrote: > Dear Karen, > The triangulation feature is a method that quickly tells you which people > are also matching a known relative or a genetic cousin whose relationship > to > you is unknown. You need to be careful how you interpret the results, > particularly when you are dealing with endogamous populations. At this > point I would suggest that you not jump to the conclusion that A and B are > related to you through the ggg grandfather that you share with your cousin. > Perhaps they are related through that line and perhaps not. I think you > need data from known first, second, and/or third cousins to help you sort > issues like this out. You need to use their data to map your dad's (and > your chromosomes) so you can have some idea where each of these segments > came from. You can then look at the matches on any one segment and can > have > better insight as to whether or not they could have come from a specific > ancestral line, such as through the ggg grandfather that you share with > your > cousin. At this point, all I would do if I were you is to enter the data > from A and B on your match list and wait for data to accumulate from other > matches at 23andMe, Family Finder, and GEDmatch to help you sort out where > the genealogical connection is on the segments you share with A and B. > Sincerely, > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges > Sent: Friday, October 18, 2013 1:42 AM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them > > Hi Tim > > My cousin and I match on Chromosome 4. This is my first DNA match besides > Dad so I haven't yet needed to map anything.Dad should match my 4th half > cousin as it is on his maternal side of the family tree but doesn't. I > share a 3G Grandfather with my cousin. I descend from the first wife and > they descend from the second. I have contacted Family tree DNA to check > that an error has not occurred and it is currently being investigated. I > don't see a genealogy connection to my Mum's tree. > > Match A matches me on chromosome 1 and Match B on chromosome 22 both are > listed as 5th to remote cousins. Dad also matches A in the same location as > I do on chromosome 1 but does not match B although he does have another > match to a person with the same surname. My cousin and I both show match A > and B when we triangulate each others name but we don't match them in the > same locations. A is also a 5th to remote cousin to my 4th half cousin > while B is a 2nd-4th cousin to them. > > What I need to understand please [with the new tools] if you find a > genealogy match with a DNA match [such as my 4th cousin] when you > triangulate with their name and find your in common with matches does it > mean these other smaller cM matches are related [IBD] because two known > related people are matching the same people. eg strengthens the odds that > it is not a coincidence? For my cousin match B is 17.15cMs so this should > be a relative of hers. but with A we all have smaller matches 8cMs. > > Karen > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Dear Karen, HIR stands for half-identical region. It is an extremely important term for genetic genealogists interested in autosomal DNA to understand well. Because I couldn't find a good definition for an HIR 9 months or so ago, I wrote my own. It is as follows: Half-identical region: a region of two paired chromosomes where at least one of the two alleles from one person's pair of chromosomes matches at least one of the two alleles from a different person's pair of chromosomes throughout the entire region. A half-identical region may be either identical by descent (IBD) or identical by state (IBS). Some scientists use IBS to mean an HIR. I think things are simpler and clearer if you use the term HIR in the right context and use IBS only for HIRs that are false matches (not the result of a shared common ancestor for the HIR in question). This topic came up on the RootsWeb DNA list in 2009 shortly after 23andMe released Relative Finder. Ann Turner's comments at http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2009-11/12572588 09 are instructive. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges Sent: Saturday, October 19, 2013 2:29 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them What is HIR short for please? Karen

Karen, I'm so sorry. I missed your second question. Half-identical Region (HIR) - a region or segment along one of the copies of a chromosome (chromosomes each have two copies, one from mom and one from dad) where at least one of the two alleles (A, G, T, C) of a person's test results matches at least one of the two alleles from a different person's test results throughout the segment. A half-identical region may be either identical by descent (IBD) or identical by state (IBS). -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges Sent: Saturday, October 19, 2013 2:29 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them Hi Emily I was wondering what a mish mash of paternal and maternal alleles was? . Your comment is much appreciated. What is HIR short for please? Karen On Sun, Oct 20, 2013 at 3:05 AM, Emily Aulicino <aulicino@hevanet.com>wrote: > Please correct me if I am wrong, but false positives (sadly, a very > general > term) are small segments that are neither identical by descent (IBD) > or identical by state (IBS) and may be a result of the way the > companies are processing the half-identical regions (HIR) information > or they may be a mish-mash of paternal and maternal alleles. > > If two people you match do not match each other, then it is only that > each of those you match are on a different chromosome (these are > different HIRs). > > E > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett > Sent: Saturday, October 19, 2013 6:17 AM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of > them > > Karen > > False positives from FF ICW can be determined by asking the two > Matches in question if they match each other on the same segment you match them. > Either > one can confirm it. > > Also you can easily compare them at GEDmatch to see if and how much > and where they share (if they'll upload to GEDmatch). > > Also you can confirm them, one at a time, if they match a close cousin > (your close cousin can confirm the segment if you don't manage their > kit). > > I would never think about comparing raw data. If they won't cooperate > at all (as above), they surely won't give you their raw data, either. > > Jim - Sent from my iPhone - FaceTime! > > On Oct 19, 2013, at 7:52 AM, Karen Hodges <rowantreek@gmail.com> wrote: > > > Hi Jim > > > > Thanks for your comments. I think I am good with the true matches > > now but the false positives can these only be determined by > > comparing the raw DNA when no genealogy match is found and is there > > a program that can > do this? > > > > Karen > > > > > > On Sat, Oct 19, 2013 at 10:12 PM, Jim Bartlett > <jim4bartletts@verizon.net>wrote: > > > >> Karen > >> > >> In general I agree with Tim. I would add that Triangulation has a > >> very specific requirement: A=B=C=A. That is each pair (AB,AC,BC) > >> must have a shared segment (usually at least 7cM, but perhaps > >> smaller with some risk of a false positive); AND each of these > >> shared segments are significantly overlapping - such that all three > >> - ABC - have, say, at > least the same 7cM. > >> You can accept a little less overlap, by accepting a little more > >> risk that it's not right. With so much randomness in atDNA, we > >> cannot guarantee anything. > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > ______________________________ For answers to Frequently Asked Questions about mailing lists, please see: http://dgmweb.net/MailingListFAQs.html ------------------------------- To unsubscribe from the list, please send an email to AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Karen I don't understand "under 7cMs matches that match only me on a > > Chromosome". At FF and GEDmatch you can get shared segments down to 1cM. Both you and your Match get exactly the same string of ACTGs, and so get a matching segment. At GEDmatch you can compare yourself 1-to-1 to anyone else there - and you can set the threshold at 1cM. It is not unusual to compare to someone who is not a Match by most algorithms, and get 10-20 small matching segments. Most of these will be IBS segments - made up by individual ACTGs from both your parents to match someone else's combination. Or it could be pieces from each parent that match someone else's pieces. As you get segments over 7cM, it's somewhat harder to mix and match like this and wind up with a match - so the larger shared segments tend to be IBD - in tact chunks directly from a Common Ancestor. And yes, when you form a Triangle of Matches, the odds are much better that the segments are IBD. And if a shared segment can't Triangulate on either parent's Chr, it's probably an IBS segment. Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 5:14 PM, Karen Hodges <rowantreek@gmail.com> wrote: > Hi Jim > > That I understand. Its the under 7cMs matches that match only me on a > Chromosome. I guess these are best put aside if there is no genealogy > connection. Or two other matches come up in the same area for comparison > to determine IBD or IBS. > > Karen >

I was responding in the context of FF ICW. I took false positives to mean cases where 2 Matches were ICW each other (seemingly positive), but turn out to be matching on a different Chr (thus not forming a Triangulated Group - i.e. false). Sorry if the context was different and I missed it. If the question is how do you detect that a reported match is really IBS. Note there are several ways to get an IBS segment, but they all have the same bottom line - an IBS segment does not come from a Common Ancestor. The way I determine an IBS segment is when that Match doesn't match others on that segment who shave already been shown to have IBD segments on both sides. In other words the IBS segment should/would match with other segments, but doesn't. I note it as a probable IBS segment, and move on to other Matches. There is so much to check and document, that I won't dwell on these stumbling blocks. Focus on more promising leads. It was my understanding that all "shared" segments (of any size) were either IBD or IBS - there is no third category?? Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 12:05 PM, "Emily Aulicino" <aulicino@hevanet.com>wrote: > Please correct me if I am wrong, but false positives (sadly, a very general > term) are small segments that are neither identical by descent (IBD) or > identical by state (IBS) and may be a result of the way the companies are > processing the half-identical regions (HIR) information or they may be a > mish-mash of paternal and maternal alleles. > > If two people you match do not match each other, then it is only that each > of those you match are on a different chromosome (these are different HIRs). > > E > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett > Sent: Saturday, October 19, 2013 6:17 AM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them > > Karen > > False positives from FF ICW can be determined by asking the two Matches in > question if they match each other on the same segment you match them. Either > one can confirm it. > > Also you can easily compare them at GEDmatch to see if and how much and > where they share (if they'll upload to GEDmatch). > > Also you can confirm them, one at a time, if they match a close cousin (your > close cousin can confirm the segment if you don't manage their kit). > > I would never think about comparing raw data. If they won't cooperate at all > (as above), they surely won't give you their raw data, either. > > Jim - Sent from my iPhone - FaceTime! > > On Oct 19, 2013, at 7:52 AM, Karen Hodges <rowantreek@gmail.com> wrote: > >> Hi Jim >> >> Thanks for your comments. I think I am good with the true matches now >> but the false positives can these only be determined by comparing the >> raw DNA when no genealogy match is found and is there a program that can > do this? >> >> Karen >> >> >> On Sat, Oct 19, 2013 at 10:12 PM, Jim Bartlett > <jim4bartletts@verizon.net>wrote: >> >>> Karen >>> >>> In general I agree with Tim. I would add that Triangulation has a >>> very specific requirement: A=B=C=A. That is each pair (AB,AC,BC) must >>> have a shared segment (usually at least 7cM, but perhaps smaller with >>> some risk of a false positive); AND each of these shared segments are >>> significantly overlapping - such that all three - ABC - have, say, at > least the same 7cM.

Karen, I'm not geneticist, but my understanding is that it is small pieces which could be a bit mixed between the parents' chromosmes. Maybe someone else can explain. I was told this by someone with some type of biology degree. E -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges Sent: Saturday, October 19, 2013 2:29 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them Hi Emily I was wondering what a mish mash of paternal and maternal alleles was? . Your comment is much appreciated. What is HIR short for please? Karen On Sun, Oct 20, 2013 at 3:05 AM, Emily Aulicino <aulicino@hevanet.com>wrote: > Please correct me if I am wrong, but false positives (sadly, a very > general > term) are small segments that are neither identical by descent (IBD) > or identical by state (IBS) and may be a result of the way the > companies are processing the half-identical regions (HIR) information > or they may be a mish-mash of paternal and maternal alleles. > > If two people you match do not match each other, then it is only that > each of those you match are on a different chromosome (these are > different HIRs). > > E > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett > Sent: Saturday, October 19, 2013 6:17 AM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of > them > > Karen > > False positives from FF ICW can be determined by asking the two > Matches in question if they match each other on the same segment you match them. > Either > one can confirm it. > > Also you can easily compare them at GEDmatch to see if and how much > and where they share (if they'll upload to GEDmatch). > > Also you can confirm them, one at a time, if they match a close cousin > (your close cousin can confirm the segment if you don't manage their > kit). > > I would never think about comparing raw data. If they won't cooperate > at all (as above), they surely won't give you their raw data, either. > > Jim - Sent from my iPhone - FaceTime! > > On Oct 19, 2013, at 7:52 AM, Karen Hodges <rowantreek@gmail.com> wrote: > > > Hi Jim > > > > Thanks for your comments. I think I am good with the true matches > > now but the false positives can these only be determined by > > comparing the raw DNA when no genealogy match is found and is there > > a program that can > do this? > > > > Karen > > > > > > On Sat, Oct 19, 2013 at 10:12 PM, Jim Bartlett > <jim4bartletts@verizon.net>wrote: > > > >> Karen > >> > >> In general I agree with Tim. I would add that Triangulation has a > >> very specific requirement: A=B=C=A. That is each pair (AB,AC,BC) > >> must have a shared segment (usually at least 7cM, but perhaps > >> smaller with some risk of a false positive); AND each of these > >> shared segments are significantly overlapping - such that all three > >> - ABC - have, say, at > least the same 7cM. > >> You can accept a little less overlap, by accepting a little more > >> risk that it's not right. With so much randomness in atDNA, we > >> cannot guarantee anything. > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message > ______________________________ For answers to Frequently Asked Questions about mailing lists, please see: http://dgmweb.net/MailingListFAQs.html ------------------------------- To unsubscribe from the list, please send an email to AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Hi Folks, I have a two parent one child trio and would like to experiment with phasing on my own, presumably using excel, but will consider other possibilities, but want to stay away from gedmatch for the time being. The child and mother have tested FF at FTDNA, and the father has tested 23andme, and imported to FTDNA. The problem is that FTDNA does not have his raw data available for me to download. Thus, it seems to me, that I need to convert his 23andme data to "FTDNA-like" data. I have all three raw data files in my possession. How do I go about converting 23andme to FTDNA? Does someone have an excel solution that I could "borrow"? And secondarily, what is normal in the case of 23andme import to FTDNA regarding raw data download from FTDNA? Do people have no trouble, or do they have to nudge FTDNA to provide the raw data from their perspective, or is it the case that even after nudging them they still can't get it? Best, Gregg P. S. I already sent an error report to FTDNA informing them of the error on attempt to retrieve raw data for this father.

Karen False positives from FF ICW can be determined by asking the two Matches in question if they match each other on the same segment you match them. Either one can confirm it. Also you can easily compare them at GEDmatch to see if and how much and where they share (if they'll upload to GEDmatch). Also you can confirm them, one at a time, if they match a close cousin (your close cousin can confirm the segment if you don't manage their kit). I would never think about comparing raw data. If they won't cooperate at all (as above), they surely won't give you their raw data, either. Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 7:52 AM, Karen Hodges <rowantreek@gmail.com> wrote: > Hi Jim > > Thanks for your comments. I think I am good with the true matches now but > the false positives can these only be determined by comparing the raw DNA > when no genealogy match is found and is there a program that can do this? > > Karen > > > On Sat, Oct 19, 2013 at 10:12 PM, Jim Bartlett <jim4bartletts@verizon.net>wrote: > >> Karen >> >> In general I agree with Tim. I would add that Triangulation has a very >> specific requirement: A=B=C=A. That is each pair (AB,AC,BC) must have a >> shared segment (usually at least 7cM, but perhaps smaller with some risk of >> a false positive); AND each of these shared segments are significantly >> overlapping - such that all three - ABC - have, say, at least the same 7cM. >> You can accept a little less overlap, by accepting a little more risk that >> it's not right. With so much randomness in atDNA, we cannot guarantee >> anything.

Please correct me if I am wrong, but false positives (sadly, a very general term) are small segments that are neither identical by descent (IBD) or identical by state (IBS) and may be a result of the way the companies are processing the half-identical regions (HIR) information or they may be a mish-mash of paternal and maternal alleles. If two people you match do not match each other, then it is only that each of those you match are on a different chromosome (these are different HIRs). E -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Jim Bartlett Sent: Saturday, October 19, 2013 6:17 AM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them Karen False positives from FF ICW can be determined by asking the two Matches in question if they match each other on the same segment you match them. Either one can confirm it. Also you can easily compare them at GEDmatch to see if and how much and where they share (if they'll upload to GEDmatch). Also you can confirm them, one at a time, if they match a close cousin (your close cousin can confirm the segment if you don't manage their kit). I would never think about comparing raw data. If they won't cooperate at all (as above), they surely won't give you their raw data, either. Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 7:52 AM, Karen Hodges <rowantreek@gmail.com> wrote: > Hi Jim > > Thanks for your comments. I think I am good with the true matches now > but the false positives can these only be determined by comparing the > raw DNA when no genealogy match is found and is there a program that can do this? > > Karen > > > On Sat, Oct 19, 2013 at 10:12 PM, Jim Bartlett <jim4bartletts@verizon.net>wrote: > >> Karen >> >> In general I agree with Tim. I would add that Triangulation has a >> very specific requirement: A=B=C=A. That is each pair (AB,AC,BC) must >> have a shared segment (usually at least 7cM, but perhaps smaller with >> some risk of a false positive); AND each of these shared segments are >> significantly overlapping - such that all three - ABC - have, say, at least the same 7cM. >> You can accept a little less overlap, by accepting a little more risk >> that it's not right. With so much randomness in atDNA, we cannot >> guarantee anything. ______________________________ For answers to Frequently Asked Questions about mailing lists, please see: http://dgmweb.net/MailingListFAQs.html ------------------------------- To unsubscribe from the list, please send an email to AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Karen In general I agree with Tim. I would add that Triangulation has a very specific requirement: A=B=C=A. That is each pair (AB,AC,BC) must have a shared segment (usually at least 7cM, but perhaps smaller with some risk of a false positive); AND each of these shared segments are significantly overlapping - such that all three - ABC - have, say, at least the same 7cM. You can accept a little less overlap, by accepting a little more risk that it's not right. With so much randomness in atDNA, we cannot guarantee anything. For example the segments themselves are not precise - the end points are often fuzzy. But it works a high percentage of the time. If you are A, and you match B and C on basically the same segment; you still need to determine if B and C share that same segment. This is fairly straightforward using tools at 23andMe or at GEDmatch. At FTDNA the ICW tool indicates if B and C have a shared segment somewhere. Often they share the same place you do, but sometimes they don't. I looked at a lot of these cases a year ago, and - from memory - about 2/3 ICW were on the same segment and 1/3 was not. Or something like that - it was high enough, for me, to investigate more, but not high enough to conclude there was Triangulation - my judgement call. So I usually ask B and C if they match on the same segment we share. Either one can confirm it. This is a simple question for them, and if they are on the same segment with you, this is very powerful information for them, too. Particularly as the Triangulated groups grow beyond 3 folks to 5 to 10 to 20... Such large groups should have enough researchers in them willing to work on place/time matching - clearly if a Common Ancestor doesn't become evident, we are dealing with a brick wall for many. When you have Triangulation, you know the shared segment (among ABC) is on one chromosome, and that the 3 of you will have a Common Ancestor. (Assuming you are one of the ABC). Now if any two in ABC have a known Common Ancestor, there is a good probability that all three of you have the same Common Ancestor. When dealing with deep Colonial roots (and similar populations) the possibility exists that you and a Match could have more than one Common Ancestor. So it's always wise to find at least one more Match who agrees on the genealogy for this segment. This means waiting for additional Matches - but don't worry, they are coming... Jim - Sent from my iPhone - FaceTime! On Oct 19, 2013, at 2:19 AM, "Tim Janzen" <tjanzen@comcast.net> wrote: > Dear Karen, > The triangulation feature is a method that quickly tells you which people > are also matching a known relative or a genetic cousin whose relationship to > you is unknown. You need to be careful how you interpret the results, > particularly when you are dealing with endogamous populations. At this > point I would suggest that you not jump to the conclusion that A and B are > related to you through the ggg grandfather that you share with your cousin. > Perhaps they are related through that line and perhaps not. I think you > need data from known first, second, and/or third cousins to help you sort > issues like this out. You need to use their data to map your dad's (and > your chromosomes) so you can have some idea where each of these segments > came from. You can then look at the matches on any one segment and can have > better insight as to whether or not they could have come from a specific > ancestral line, such as through the ggg grandfather that you share with your > cousin. At this point, all I would do if I were you is to enter the data > from A and B on your match list and wait for data to accumulate from other > matches at 23andMe, Family Finder, and GEDmatch to help you sort out where > the genealogical connection is on the segments you share with A and B. > Sincerely, > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges > Sent: Friday, October 18, 2013 1:42 AM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them > > Hi Tim > > My cousin and I match on Chromosome 4. This is my first DNA match besides > Dad so I haven't yet needed to map anything.Dad should match my 4th half > cousin as it is on his maternal side of the family tree but doesn't. I > share a 3G Grandfather with my cousin. I descend from the first wife and > they descend from the second. I have contacted Family tree DNA to check > that an error has not occurred and it is currently being investigated. I > don't see a genealogy connection to my Mum's tree. > > Match A matches me on chromosome 1 and Match B on chromosome 22 both are > listed as 5th to remote cousins. Dad also matches A in the same location as > I do on chromosome 1 but does not match B although he does have another > match to a person with the same surname. My cousin and I both show match A > and B when we triangulate each others name but we don't match them in the > same locations. <snip>

Dear Karen, The triangulation feature is a method that quickly tells you which people are also matching a known relative or a genetic cousin whose relationship to you is unknown. You need to be careful how you interpret the results, particularly when you are dealing with endogamous populations. At this point I would suggest that you not jump to the conclusion that A and B are related to you through the ggg grandfather that you share with your cousin. Perhaps they are related through that line and perhaps not. I think you need data from known first, second, and/or third cousins to help you sort issues like this out. You need to use their data to map your dad's (and your chromosomes) so you can have some idea where each of these segments came from. You can then look at the matches on any one segment and can have better insight as to whether or not they could have come from a specific ancestral line, such as through the ggg grandfather that you share with your cousin. At this point, all I would do if I were you is to enter the data from A and B on your match list and wait for data to accumulate from other matches at 23andMe, Family Finder, and GEDmatch to help you sort out where the genealogical connection is on the segments you share with A and B. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges Sent: Friday, October 18, 2013 1:42 AM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] Family finder matches what to make of them Hi Tim My cousin and I match on Chromosome 4. This is my first DNA match besides Dad so I haven't yet needed to map anything.Dad should match my 4th half cousin as it is on his maternal side of the family tree but doesn't. I share a 3G Grandfather with my cousin. I descend from the first wife and they descend from the second. I have contacted Family tree DNA to check that an error has not occurred and it is currently being investigated. I don't see a genealogy connection to my Mum's tree. Match A matches me on chromosome 1 and Match B on chromosome 22 both are listed as 5th to remote cousins. Dad also matches A in the same location as I do on chromosome 1 but does not match B although he does have another match to a person with the same surname. My cousin and I both show match A and B when we triangulate each others name but we don't match them in the same locations. A is also a 5th to remote cousin to my 4th half cousin while B is a 2nd-4th cousin to them. What I need to understand please [with the new tools] if you find a genealogy match with a DNA match [such as my 4th cousin] when you triangulate with their name and find your in common with matches does it mean these other smaller cM matches are related [IBD] because two known related people are matching the same people. eg strengthens the odds that it is not a coincidence? For my cousin match B is 17.15cMs so this should be a relative of hers. but with A we all have smaller matches 8cMs. Karen

Hi Tim My cousin and I match on Chromosome 4. This is my first DNA match besides Dad so I haven't yet needed to map anything.Dad should match my 4th half cousin as it is on his maternal side of the family tree but doesn't. I share a 3G Grandfather with my cousin. I descend from the first wife and they descend from the second. I have contacted Family tree DNA to check that an error has not occurred and it is currently being investigated. I don't see a genealogy connection to my Mum's tree. Match A matches me on chromosome 1 and Match B on chromosome 22 both are listed as 5th to remote cousins. Dad also matches A in the same location as I do on chromosome 1 but does not match B although he does have another match to a person with the same surname. My cousin and I both show match A and B when we triangulate each others name but we don't match them in the same locations. A is also a 5th to remote cousin to my 4th half cousin while B is a 2nd-4th cousin to them. What I need to understand please [with the new tools] if you find a genealogy match with a DNA match [such as my 4th cousin] when you triangulate with their name and find your in common with matches does it mean these other smaller cM matches are related [IBD] because two known related people are matching the same people. eg strengthens the odds that it is not a coincidence? For my cousin match B is 17.15cMs so this should be a relative of hers. but with A we all have smaller matches 8cMs. Karen On Fri, Oct 18, 2013 at 4:37 PM, Tim Janzen <tjanzen@comcast.net> wrote: > Dear Karen, > You haven't really given me enough information here to help me sort > this out. Do A and B match each other on the same location that you match > your half 4th cousin matches you on? If not, I don't think that their > information is all that helpful to you. Are you keeping a detailed match > list like the one I have for my mom at > > https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20 > for%20Betty%20Janzen%20(public).xls? Have you tested a parent or a child > yet? If so, does that parent or child match your half 4th cousin? If so, > do they match A and/or B on the same segment? Make sure you are mapping > the > data from this half 4th cousin. > Tim Janzen > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges > Sent: Thursday, October 17, 2013 6:30 AM > To: autosomal-dna@rootsweb.com > Subject: [AUTOSOMAL-DNA] Family finder matches what to make of them > > We know from genealogy research we are fourth half cousins [Our 3xG > Grandfather was married twice and we descend from a different wife]. My new > found cousin has two matches which I will call A and B when she > triangulates my match. I have the same two matches when I triangulate with > her DNA. A and B and my 4th cousin do not match in the same locations. A > and B are over 8cM matches to me and are listed as 5th to remote cousins. > > Are A and B, IBD because I match my 4th cousin who has the same matches > although in different locations? Or could it just be a coincidence we have > matches in common who are unrelated to us? > > Unsure > Karen > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Dear Greg, You need to always keep in mind precisely what your goals are with autosomal DNA testing. You are always trying to do two primary things: 1. You are trying to confirm your (or someone else's) family tree. 2. You are trying to extend your (or someone else's) family tree. To do the above you need to be carefully mapping your genomes as well as that of your close relatives. In your case, you want to be mapping the genome of your cousin's parent who is biologically related to you. You do that just exactly in the same way you would map the genome of your parents. What you really want to have at GEDmatch are the phased data files of the parent of your cousin who is biologically related to you (your aunt or your uncle). There should be two files, one for each set of autosomal chromosomes. You then want to be entering the data from the people who are matching one of those two files into your match list. I mentioned my mom's match list at https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20 for%20Betty%20Janzen%20(public).xls earlier this evening as an example of what you should be keeping. You then want to be creating a chromosome map for anyone you have found a genealogical connection with whose data you feel comfortable mapping. This would be similar to the one for my mom at https://dl.dropboxusercontent.com/u/21841126/phased%20genome%20of%20Robert%2 0and%20Betty%20Janzen%20(public).zip. If you aren't yet comfortable with chromosome mapping, I suggest you review the document that Emily Aulicino and I wrote at https://dl.dropboxusercontent.com/u/21841126/Basics%20of%20Chromosome%20Mapp ing.docx. So in summary, the sequence of the things you need to do in terms of GEDmatch are as follows: 1. Upload two phased data files of the parent of your cousin who is biologically related to you to GEDmatch. Use David Pike's utility or mine at https://dl.dropboxusercontent.com/u/21841126/phasing%20program%20(small%20ve rsion).xls to generate the phased data if you need to. 2. Record all of the matching segment data for each of these two phased data files in GEDmatch. 3. Get the pedigree charts for each of the matches (preferably as GEDCOMs). 4. Look for shared genealogical connections for everyone who is matching on the same segment. 5. When you are convinced of the ancestry of any particular segment then record that information on the chromosome map. GEDmatch doesn't allow you to download your phased data files for your personal use. It only creates them for you on their system. Keep in mind that GEDmatch is only creating one of the two phased files for each of the parents of your cousin. You need to create and upload the second one for each parent on your own. Yes, you can get cleaned phased data files if you phase the data yourself. You need to run a program in Excel or in some other way determine which SNPs are discordant. I have a phasing discrepancy file in Excel that I wrote specifically for this purpose. You will generally find about 200 to 300 SNPs that are discrepant in a two-parent/one child trio. You want to remove the data for all of these SNPs from your phased data files before you upload them to GEDmatch. The phased data files you want to upload to GEDmatch will only have a single allele value for each SNP. You may need to correspond directly with John Olson at GEDmatch at GEDmatch@gmail.com if you have any problems uploading your phased data files. What you will know when you are using phased data files at GEDmatch rather than simply unphased ones are which of the HIRs are IBD and which are IBS. Quite a few of the HIRs under 10 cMs are IBS. Using phased files helps you eliminate those from consideration in your match list. Keep in mind that when you are using phased files from a two-parent/one child trio you won't know where all of the crossovers are. Thus, there will be a few HIRs that are IBD that will be picked up when you are running the comparisons with an unphased file that won't be picked up when running the comparison using the phased file. The only way to sort that out is to do extensive chromosome mapping using data from first and second cousins so that you can determine approximately where the crossovers are. Then eliminate 25 to 50 SNPs on each side of where you believe the crossovers are and insert a "-" in your phased file in that region. Then put the correct phased data in each file. For instance, if you have extensively mapped the data for one of your cousin's parents, then put the data for one of the cousin's grandparents in one file and put the data for the other cousin's grandparent in the second file. Relatively few people can do that because they don't know where very many of these crossovers are. I know where about 80% of the crossovers are for my mom because I have mapped just over 80% of her genome at this point. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Gregg Bonner Sent: Thursday, October 17, 2013 10:03 PM To: autosomal-dna@rootsweb.com Subject: [AUTOSOMAL-DNA] Application of phased files from two parent one child trio My principle question is...what is the order of operations to follow using the pair of phased files to extract whatever data will "fall out" of the data itself? What I am principally interested in is using the files to reduce the number of false positive matching segments in the list of _"P"_. Is that possible, and if so, how do you go about doing it? Is it an excel solution followed by re-upload of yet another file to gedmatch? My other questions are about file input/output in gedmatch. Can we download any of the raw data files? Is the user offered a chance to download the phased files upon creation, or do they reside always at gedmatch only? It seems this should offer genotyping error cleaning. Is there a way to get "cleaned" output of a raw file based on the trio? And regarding input, is it the case in gedmatch usage that the "raw" file can be the RS number followed by either 1 or 2 letters, or a dash, or is it the case that the phased file has every phased RS appearing homozygous so that the input still has two characters per row? Just for completeness, I want to quote "M" - "What do I do with these results [i.e., the phased files]? And what will I know that I did not know before?" Gregg

I am not sure how to ask this question but am wondering if the below means anything. I have found my first DNA match! We know from genealogy research we are fourth half cousins [Our 3xG Grandfather was married twice and we descend from a different wife]. My new found cousin has two matches which I will call A and B when she triangulates my match. I have the same two matches when I triangulate with her DNA. A and B and my 4th cousin do not match in the same locations. A and B are over 8cM matches to me and are listed as 5th to remote cousins. Are A and B, IBD because I match my 4th cousin who has the same matches although in different locations? Or could it just be a coincidence we have matches in common who are unrelated to us? Unsure Karen

Dear Karen, You haven't really given me enough information here to help me sort this out. Do A and B match each other on the same location that you match your half 4th cousin matches you on? If not, I don't think that their information is all that helpful to you. Are you keeping a detailed match list like the one I have for my mom at https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20 for%20Betty%20Janzen%20(public).xls? Have you tested a parent or a child yet? If so, does that parent or child match your half 4th cousin? If so, do they match A and/or B on the same segment? Make sure you are mapping the data from this half 4th cousin. Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Karen Hodges Sent: Thursday, October 17, 2013 6:30 AM To: autosomal-dna@rootsweb.com Subject: [AUTOSOMAL-DNA] Family finder matches what to make of them We know from genealogy research we are fourth half cousins [Our 3xG Grandfather was married twice and we descend from a different wife]. My new found cousin has two matches which I will call A and B when she triangulates my match. I have the same two matches when I triangulate with her DNA. A and B and my 4th cousin do not match in the same locations. A and B are over 8cM matches to me and are listed as 5th to remote cousins. Are A and B, IBD because I match my 4th cousin who has the same matches although in different locations? Or could it just be a coincidence we have matches in common who are unrelated to us? Unsure Karen

My apologies for a topic which I am sure has already been addressed, nevertheless: I have a cousin "C" who has had her autosomal DNA tested by FTDNA, as have her parents "P" and "M". All three raw files were uploaded to gedmatch, and a pair of phased files was generated with respect to "C". The phasing was performed at gedmatch by "M". What now? My principle question is...what is the order of operations to follow using the pair of phased files to extract whatever data will "fall out" of the data itself? What I am principally interested in is using the files to reduce the number of false positive matching segments in the list of _"P"_. Is that possible, and if so, how do you go about doing it? Is it an excel solution followed by re-upload of yet another file to gedmatch? My other questions are about file input/output in gedmatch. Can we download any of the raw data files? Is the user offered a chance to download the phased files upon creation, or do they reside always at gedmatch only? It seems this should offer genotyping error cleaning. Is there a way to get "cleaned" output of a raw file based on the trio? And regarding input, is it the case in gedmatch usage that the "raw" file can be the RS number followed by either 1 or 2 letters, or a dash, or is it the case that the phased file has every phased RS appearing homozygous so that the input still has two characters per row? Just for completeness, I want to quote "M" - "What do I do with these results [i.e., the phased files]? And what will I know that I did not know before?" In short, I'd like like to know the application of phased files that extends beyond the simple notion that a match in "C" should have had to have come from either "P" or "M". Cheers, Gregg

Barbara I spoke too soon. Found it. Thanks for mentioning it! Hausa On Oct 15, 2013, at 7:51 PM, karenhappuch <karenhappuch@cox.net> wrote: > Emily, > Jim Barlett is the admin of the Northern Neck Virginia project. This > project was promoted originally as atDNA and also y and mt. I'm a member of > this project and was hoping Jim would respond to your post. The project is > located at FTDNA and is open to people having ancestors from the Northern > Neck counties (6 counties). > > Barbara > > ----- Original Message ----- > From: "Emily Aulicino" <aulicino@hevanet.com> > To: <autosomal-dna@rootsweb.com> > Sent: Monday, October 14, 2013 3:24 PM > Subject: [AUTOSOMAL-DNA] atDNA Projects > > > Greetings! > > I'm looking for admins who run autosomal DNA projects (Family Finder, DNA > Relatives, AncestryDNA) to learn about how you structure them. > > I know there are some out there, but access to viewing them is not possible > through typical means. I know many other Admins allow FF tests to be a part > of their surname (or whatever) project, but I'm looking for projects that > are strictly for autosomal testing. > > A few questions: > Is your project set-up at FTDNA and/or your own website? > What are the parameters of the project? (i.e., all descendants from a > certain 4th great-grandparents) > What criteria is used to include testers as not everyone will match the > targeted ancestors? > > Other nuances of the project? > > Many thanks! > Emily > If you do not hear from me in a timely manner, just write again...I was > buried in email. LOL > http://writingyourmemories.blogspot.com/ > http://www.rootsweb.com/~orgco2/speaker/EmilyAulicino.html > http://genealem-geneticgenealogy.blogspot.com/ > Northwest Regional Coordinator and Speaker for ISOGG (www.isogg.org) > Administrator for thirteen FTDNA DNA Projects > > > > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the > quotes in the subject and the body of the message > > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message

Barbara Can you provide more specificity on the name of the Northern Neck VA project? I can not find it on FTDNA and would love to join. Thank you Hausa On Oct 15, 2013, at 7:51 PM, karenhappuch <karenhappuch@cox.net> wrote: > Emily, > Jim Barlett is the admin of the Northern Neck Virginia project. This > project was promoted originally as atDNA and also y and mt. I'm a member of > this project and was hoping Jim would respond to your post. The project is > located at FTDNA and is open to people having ancestors from the Northern > Neck counties (6 counties). > > Barbara >