Felix Immanuel has written a utility to perform a similar function. I have not used it myself, but I have noted difficulties with some of his other utilities. I'd be interested in a comparison of your results with his. http://www.y-str.org/2013/08/dna-error-fix.html A priori, I would not expect a huge impact on the one-to-many match function. The additional SNPs with data would help increase the tally for the SNP threshold, but any effect would be scattered over the whole genome. You may already have done this, but I'd recommend designating some of your "duplicate" kits as research. That way you can do your own experiments but not show up multiple times in the list of your matches. I'm looking forward to hearing your conclusions. Ann Turner On Mon, Dec 14, 2015 at 8:47 PM, David Schroeder via < genealogy-dna@rootsweb.com> wrote: > I was able to 'fix' the no-calls for matching RSIDs on both Ancestry and > 23andme when one, or the other, was not a no-call. I fixed 6,632 on 23andme > and 6,708 on Ancestry. > > Interestingly enough, there were 3,833 that were left as no-calls on both > 23andme and AncestryDNA for the same RSIDs. I am wondering if these are the > result of particularly difficult locations to test, or perhaps the SNP is > rare in my genome? The tests were over two years apart. > > I uploaded both fixed raw data files to gedmatch to see how it may affect > my > 'one-to-many' matches. (Will have to wait on the processing). I ran the > Gedmatch File Diagnostic Utility, and the fixed files had significantly > reduced my error rates. It seems that most of my errors are in the X, Y or > MT Chromosomes. > > David > > ------------------------------ > > Message: 4 > Date: Sun, 13 Dec 2015 03:31:45 -0800 > From: Ann Turner <dnacousins@gmail.com> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs > AncestryDNA > To: DNA Genealogy Mailing List <genealogy-dna@rootsweb.com> > Message-ID: > < > CAA-Ub_COJUEcMV4v3aXj4hbEaj6cbFf01AT9yDSBMJwDoyTnsA@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > I've always mentally thought about the "i" SNPs as "internal" catalog > numbers, but I'm not positive if I made that up or actually noticed someone > from 23andMe used that word :) > > As you probably noticed, AncestryDNA doesn't always present alleles in > alphabetical order. You will find instances of TC and CT, for example. > Illumina's base-calling software has something called a "top strand" and a > "bottom strand" (not the same thing as forward/reverse or plus/minus). > 23andMe does some post-processing to put alleles in alphabetical order. > Anyway, did you also look for TA? > > SNPs where the alternative alleles are also complementary base pairs in the > double helix ( A <-> T and C <-> G) are tricky to handle. 23andMe may have > developed custom probes to identify some of those. > > I've also noticed that AncestryDNA and FTDNA do not report any indels (the > I and D alleles you asked about). > > Tim, this may not be worth the effort to analyze, but I'm curious to know > if the "i" variants with rs numbers at FTDNA may be cases where 23andMe put > some additional probes on the chip for a particular locus. If you have a > list handy, I could explore that a bit. > > Ann Turner > > > > > > Ann Turner > > On Sat, Dec 12, 2015 at 11:41 PM, Tim Janzen via < > genealogy-dna@rootsweb.com > > wrote: > > > Dear David, > > DD means a deletion and II means an insertion. The "i" SNPs in > the > > 23andMe files are those that don't have rs numbers assigned to them by > > 23andMe. It is possible that "i" stands for Illumina, but I am not > certain > > about that. It is also possible that it stands for "inserted", possibly > > because 23andMe inserted these SNPs onto the SNP chip because they were > of > > special interest to 23andMe. Someone at 23andMe would know the answer to > > this question. > > It is interesting that AncestryDNA files don't have SNPs with the > > allele values AT. I don't have a definite answer for that. I checked my > > mom's file for the SNPs that have the allele values AT in 23andMe and > found > > a total of 322 of these SNPs. I then checked for these SNPs in my mom's > > AncestryDNA file and I couldn't find any of those SNPs in my mom's > > AncestryDNA file. My suspicion is that Ancestry.com has dropped all SNPs > > from their dataset with the values AT because they think that the results > > may be erroneous. > > Sincerely, > > Tim Janzen > > > > -----Original Message----- > > From: genealogy-dna-bounces@rootsweb.com > > [mailto:genealogy-dna-bounces@rootsweb.com] On Behalf Of David Schroeder > > via > > Sent: Saturday, December 12, 2015 9:33 PM > > To: genealogy-dna@rootsweb.com > > Subject: [DNA] My Raw Data Files - Comparison 23andme vs AncestryDNA > > > > I have tested at both 23andme (V3) and AncestryDNA. I have written a > > program > > to add the raw data file information into a MySQL database, creating > > separate tables for my 23andme results and my AncestryDNA. > > > > I am trying to understand some things. > > > > I can understand all the A, C, G, T lettering. The single letters > represent > > SNPs on my Y and X chromosomes. I also understand that '--' is a no call. > > What are 'DD' and 'II'? > > > > > > I also found that AncestryDNA had no 'AT' SNPs for me, but 23andme had > 611: > > > > Can anyone explain why I have no 'AT' SNP pairs in my AncestryDNA raw > data > > file? I verified this by browsing my Ancestry Raw data file. I had every > > other SNP pair represented. > > > > The final question is about RSIDs. What are the ones that begin with 'i' > in > > my 23andme raw data file? I have 10,709 RSIDs that begin with 'i-----'. > > > > David > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > > the quotes in the subject and the body of the message > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >