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I noticed today (1 Jun 2016) that AncestryDNA.com has converted over to their new 2.0 file format, where as about a week ago they were still on the 1.0 format.

Both file formats state they are based on build 37.1 but FamilyTreeDNA.com is not accepting their transfers.

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How does one convert between the two formats as the format at face value seems to be the same?

AncestryDNA raw data download This file was generated by AncestryDNA at: 05/31/2016 17:22:49 MDT Data was collected using AncestryDNA array version: V2.0 Data is formatted using AncestryDNA converter version: V1.0 Below is a text version of your DNA file from Ancestry.com DNA, LLC. THIS INFORMATION IS FOR YOUR PERSONAL USE AND IS INTENDED FOR GENEALOGICAL RESEARCH ONLY. IT IS NOT INTENDED FOR MEDICAL, DIAGNOSTIC, OR HEALTH PURPOSES. THE EXPORTED DATA IS SUBJECT TO THE AncestryDNA TERMS AND CONDITIONS, BUT PLEASE BE AWARE THAT THE DOWNLOADED DATA WILL NO LONGER BE PROTECTED BY OUR SECURITY MEASURES. WHEN YOU DOWNLOAD YOUR RAW DNA DATA, YOU ASSUME ALL RISK OF STORING, SECURING AND PROTECTING YOUR DATA. FOR MORE INFORMATION, SEE ANCESTRYDNA FAQS. Genetic data is provided below as five TAB delimited columns. Each line corresponds to a SNP. Column one provides the SNP identifier (rsID where possible). Columns two and three contain the chromosome and basepair position of the SNP using human reference build 37.1 coordinates. Columns four and five contain the two alleles observed at this SNP (genotype). The genotype is reported on the forward (+) strand with respect to the human reference. rsid chromosome position allele1 allele2

AncestryDNA Build 1.0

AncestryDNA raw data download This file was generated by AncestryDNA at: 05/21/2016 13:02:53 MDT Data was collected using AncestryDNA array version: V1.0 Data is formatted using AncestryDNA converter version: V1.0 Below is a text version of your DNA file from Ancestry.com DNA, LLC. THIS INFORMATION IS FOR YOUR PERSONAL USE AND IS INTENDED FOR GENEALOGICAL RESEARCH ONLY. IT IS NOT INTENDED FOR MEDICAL OR HEALTH PURPOSES. THE EXPORTED DATA IS SUBJECT TO THE AncestryDNA TERMS AND CONDITIONS, BUT PLEASE BE AWARE THAT THE DOWNLOADED DATA WILL NO LONGER BE PROTECTED BY OUR SECURITY MEASURES. WHEN YOU DOWNLOAD YOUR RAW DNA DATA, YOU ASSUME ALL RISK OF STORING, SECURING AND PROTECTING YOUR DATA. FOR MORE INFORMATION, SEE ANCESTRYDNA FAQS. Genetic data is provided below as five TAB delimited columns. Each line corresponds to a SNP. Column one provides the SNP identifier (rsID where possible). Columns two and three contain the chromosome and basepair position of the SNP using human reference build 37.1 coordinates. Columns four and five contain the two alleles observed at this SNP (genotype). The genotype is reported #on the forward (+) strand with respect to the human reference. rsid chromosome position allele1 allele2

The data looks approximately the same at the head of the data as well as at the tail in general format EXCEPT:

  1. That the new v2.0 download files now contain Chromosome 1-26 vs. the v1.0 contained Chromosomes 1-25.
  2. There are about 50,000 lines less in v2.0 what has traditional 700100 in v1.0.
  3. I know some of the SNPs Ancestry.com was testing for were deleted and replaced with different SNPs.

My initial assumption is that it is not as simple as deleting what is labeled as Chromosome 26 as there would be even less rows, which will further increase the risk of decreasing my matches (I assume).

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3 Answers 3

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The only utility I know of that converts autosomal files is Autosomal DNA Converter by Felix Immanuel.

The V2.0 change is new and happened only a few months ago. This utility would need to be updated to perform this function. Unfortunately, the author stopped updating his DNA utilities a few years ago. But if you need this conversion done, you could contact him and see if he'd be willing and able to update his program.

The hard way is to reverse engineer it, as you started doing at the end of your question. I would expect Mr. Immanuel would be good at that, and maybe he would help you if you contact him.

But do note what Roberta Estes said:

Both Family Tree DNA and GedMatch will need to see the new file formats first and have some time to work with them. We don’t know if quality of matching will be an issue given that nearly half of the SNPs are being replaced – but until we hear otherwise from either company, I’d presume that they will make every effort to accommodate the new file structure.

FamilyTreeDNA does now state that they are working on accepting the newest AncestryDNA format in the very near future. So you might want to wait until that option is available:

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  • It has been saying "very near future" since early June and I ask them almost weekly when that actually with be and they say they have absolute no ETA or if it will be supported. The 23andMe format changed a few years back and they still do not support that. I figured out how to do some conversions between sites of different formats manually without the use of a tool but not yet for the Ancestry v2 to ftDNA.
    – CRSouser
    Commented Sep 28, 2016 at 15:21
  • Obviously, the new version must be giving them problems and likely has some major incompatiblities with their DNA representation. They'll either find some way to reshape the AncestryDNA V2 data into their own form, or they will not and eventually admit that they cannot translate the data well enough. The latter case would mean that to get your data into FamilyTreeDNA, you'd have to re-test with them. The same translation problems would prevent you from being able to convert from V2 to V1.
    – lkessler
    Commented Sep 28, 2016 at 17:08
  • I suspect its more a IT resource issue which they are famous for lacking but Ive also read it might require them to modify their matching algorithm/cM calculator. Lots of active discussion on it right now on other sites.
    – CRSouser
    Commented Sep 28, 2016 at 17:14
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Ancestry DNA tests processed after May 2016 by the V4 chip. There is still not a projected date when the update will take place as of today (9/28/2016).

While not the apples to apples conversion you are looking for, you might try uploading your Ancestry DNA file to GEDMATCH. There are several useful resources there.

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Chromosome 26 are the two pseudoautosomal regions PAR1 and PAR2 (see https://en.wikipedia.org/wiki/Pseudoautosomal_region). Only AncestryDNA seems to export this data. Chromosome 23 is the 'X' and 24 is the 'Y', 25 are a few mtDNA marker.

Hope this helps,

Andreas

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