Any chance to get the code that you used to do this? -----Original Message----- From: David Schroeder via <genealogy-dna@rootsweb.com> To: genealogy-dna <genealogy-dna@rootsweb.com> Sent: Mon, Dec 14, 2015 8:50 pm Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs AncestryDNA 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