Hi David, I was wondering if we can identify by SNP count (by segment age from my cousin calculator). RE: > These matches are with people I am not related to. Form me, it is chromosome 15 from positions 233,000 to 293,000 where I have several hundred matches. Can you give a couple of examples with start and end locations, along with cMs and SNP counts for the segments(s)?? - Dave Hamm HAM DNA Project coordinator RE: On 12/18/2015 9:20 PM, genealogy-dna-request@rootsweb.com wrote: > Date: Fri, 18 Dec 2015 13:01:32 -0600 > From: "David Schroeder"<dschroed991@sbcglobal.net> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs, > AncestryDNA > To:<genealogy-dna@rootsweb.com> > Message-ID: <003a01d139c6$831bf390$8953dab0$@net> > Content-Type: text/plain; charset="us-ascii" > > Dave, > > "I was wondering what you were defining as a 'pile-up.'?" I am defining a > pileup as an extraordinary number of matches on a particular segment region. > These matches are with people I am not related to. Form me, it is chromosome > 15 from positions 233,000 to 293,000 where I have several hundred matches. > > "I am curious if you have crossed checked the reductions against what > surnames go missing?" Not yet, in the planning stages after the holidays. > > "Alternatively, have you counted the number of the pile-up of surnames as > well?" Not yet. I have explored enough matches in my pileup region to know > that there is no way most, if not all, of these people are related to me. > The pileups seem to show up in gedmatch, but it looks like 23andme > eliminated my pileup matches in DNA Relatives. > > David > > > Ann, > "You speak of fixing errors -- I assume you're referring to no-calls rather > that outright errors (miscalls)?" Yes fixing no-calls. There were only 106 > wrong-call between Ancestry and 23. Since I had over 3500 AA, TT, CC and GG > that were no-calls in either 23 or ancestry, I would think that a > significant number would be opposite homozygote which would break the > segment, and reduce the number of matches. > > David > > Date: Thu, 17 Dec 2015 15:15:34 -0500 > From: Dave Hamm<odoniv@earthlink.net> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs, > AncestryDNA > To:genealogy-dna@rootsweb.com > Message-ID:<567317E6.2010300@earthlink.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi David, > > Oh, I was wondering what you were defining as a 'pile-up.' > > I did not appear to be having such a problem, and could think of several > scenarios of what you could be referring to. I was thinking of your > efinition of a 'pile-up' as in the HLA regions. (I identify those with a > simple calculation that includes the number of SNPS....) > > Now I get it. > > I am now thinking that you are looking at your surname signature(?). > Or, at worst, haplotype group signature(?). > > I get chromosomes with a high density of matching (tiny) segments on > chromosomes 1 and 11 when using autosomal sampling from my Y-DNA surname > project. > > I am thinking that I am looking at that as a basic signature for my surname, > because of the criteria I use to match each segment triad. > > Those segments that I do not use in the triad include at least one HLA > region on chromosome 6. That HLA region (in my small study) occurs in about > 25% of my sampling (after processing). Hence the confusion for me in what > you were using for the term 'pile-up.' Apparently, I would gather that a > pile-up such as in an HLA region is not what you are referring to. > > I would think that you may be working on a method that might very well > refine your targeted matching segments. > > I am curious if you have crossed checked the reductions against what > surnames go missing? > > Alternatively, have you counted the number of the pile-up of surnames as > well? > > (I am thinking that losing a random pool of names might be an indication of > progress.) > > Or am I still not understanding the definition (as used here) for a pile-up > region? > > - Dave Hamm > > > Message: 3 > Date: Thu, 17 Dec 2015 13:32:05 -0800 > From: Ann Turner<dnacousins@gmail.com> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs > AncestryDNA > To: David Schroeder<dschroed991@sbcglobal.net>, DNA Genealogy > Mailing > List<genealogy-dna@rootsweb.com> > Message-ID: > <CAA-Ub_AMPi1C0iL97yx4joW7k--BSP99_TszhRM+BjSg1RerRw@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > GEDmatch "tokenizes" the data in an attempt to make it more uniform across > platforms, so that should not be an issue for most SNPs. All C's are > converted to G's and all A's are converted to T's (or maybe the opposite > direction, but you get the idea). That fixes any strand orientation > problems, but it introduces a few cases where the alternative alleles are > also complementary base pairs in the double helix. The next effect of that > is to give you a free ride for those few SNPs where you and your match are > really opposite homozygotes. > > You speak of fixing errors -- I assume you're referring to no-calls rather > that outright errors (miscalls). No-calls don't break up segments, just > opposite homozygotes (e.g. CC in one party and TT in the other party). > GEDmatch doesn't give any credit for the SNP threshold (although 23andMe and > FTDNA do). For that reason, I predicted you might have a small increase in > the number of matches, and I am puzzled as to why you saw a decrease. > > Ann Turner