GEDmatch will produce a phased file from one parent and one child --------------------------------------------------------------- Kitty Munson Cooper, web developer,programmer, San Diego,CA genetic genealogy blog at http://blog.kittycooper.com/ family history and genealogy at http://kittymunson.com On Thu, Dec 17, 2015 at 9:49 AM, David Schroeder via < genealogy-dna@rootsweb.com> wrote: > Ann, I am using the V3 23andme chipset. I was not expecting such major > differences in my number of matching segments- 23 vs ANCDNA- but that may > be > a good thing since a large number of my 23 matches are coming from a > pileup > region on chromosome 15, but AncestryDNA has far fewer on 15. I expected a > reduction in the number of segment matches using raw data files with a > lower > error rate. Since there were big differences, I decided to upload my > original AncestryDNA raw data for another comparison. I will do more > comparisons. The original AncestryDNA kit has a 2.0% error rate, and the > fixed has 1.0%. > > Tim, my daughter took the test and she is on gedmatch, and I have access to > her raw data. (Actually, I have two daughters who have taken the test). > Most phasing programs require a 'triple': two parents and a child. How do I > phase my data without the other parent? I could possibly use both of my > daughters' raw data to phase mine. > > The holidays are upon us, and my free time has disappeared. I am thinking > of > doing some scripts where I have all 4 kit segment matches: two from 23, > (fixed and original), and two from AncestryDNA. One thought was to > calculate > the differences in cMs for all the kits. Also, a histogram of number of > matches for each additional cM >5. I would end up with a spreadsheet with > all 4 kits, and matches on each row. Any ideas what else might be > beneficial. Also, I am 2nd generation from European immigrants. I do not > have a lot of close matches since I have no U.K. or American ancestry. > > David > > Message: 8 > Date: Wed, 16 Dec 2015 15:54:55 -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_C+BHc432aHZGOKJ1fOFNfOrwfMoVqrzS= > mkoytrvXbFQ@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > One possible explanation: If you are using v3 data, there are ~ 1,000,000 > SNPs to use when you're comparing M kits with M kits. A kits have only > 700,000 SNPs available for comparison, so it's harder to reach the SNP > threshold. > > But I'm puzzled that there was a reduction from your original M kit to the > fixed M kit. That implies that at least some of the fixes created opposite > homozygotes between potential matches. Could you do a few one-to-one > comparisons of the dropouts with different SNP and mismatch thresholds? > > Ann Turner > > Message: 10 > Date: Wed, 16 Dec 2015 23:59:28 -0800 > From: "Tim Janzen" <tjanzen@comcast.net> > Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs > AncestryDNA > To: <genealogy-dna@rootsweb.com> > Message-ID: <0bb901d138a0$daddb220$90991660$@net> > Content-Type: text/plain; charset="us-ascii" > > Dear David, > Do you have family phased data that you can upload to GEDmatch? In my > opinion it is much more important that you upload phased data to GEDmatch > than that you fix your no calls. Fixing any errors you have in your data > is > important, particularly when you moved to phased data. If you are married > and have a child then generating phased data is fairly easy. Your IBS > pileups should be dramatically reduced once you move to phased data. > Sincerely, > Tim Janzen > > > ------------------------------- > 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 >