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I have recently read that you can use third party tools like Morley's DNA and Cladefinder to generate your haplogroup from Raw DNA.

SInce you get no haplogroup info from Ancestry, do they bother sequencing the Y chromosome, and if so how detailed are the results if you import their Raw DNA into something like Morley's DNA? Would they be as detailed and granular as the subclade info you get from 23andMe, which is quite deep?

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First a comment on terminology – AncestryDNA and none of the autosomal DNA testing companies do "DNA sequencing". They do use single nucleotide polymorphisms (SNP) and/or short tandem repeats (STR) testing to look at areas of common variation in the genome. But just to be clear, these companies are not doing sequencing of any significant part of your DNA. The exception would be full sequence mitochondrial DNA testing (because the length of mtDNA is comparatively so short). Whole genome sequencing, while quickly becoming cheaper and more accessible, is not (yet) widely used for genetic genealogy.

AncestryDNA and some of the other DNA companies do test a small number of YDNA SNPs as part of their autosomal test chip. Looking at my AncestryDNA raw file there are 1704 Y-DNA SNPs tested, which can in some cases be used to predict a rough Y-DNA haplogroup (this number of SNPs is less than the several thousand SNPs tested on other chromosomes). Note that in my case the subclade prediction on Morley's DNA tool was not correct once I had my Y-DNA later tested. I cannot comment on comparison to 23andMe as I have not tested with them.

I would say that while the Y-DNA prediction tools can be interesting they are no alternative to a Y-DNA specific test.

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  • Thanks Harry. Would you be able to explain how you figured out the number of SNPs from your Raw DNA file? I'd like to know how many I got from my 23andMe test. – Charlie Oct 25 '20 at 20:47
  • The raw data should list each SNP tested by chromosome number. In my AncestryDNA file Y-DNA is recorded as chromosome 24 and 25 (they split it into pseusoautosomal and non-pseudoautosomal). Chromosome 23 is X-DNA and 26 is mitochondrial DNA SNPs. Not sure if 23andMe do it the same way. – Harry V. Oct 25 '20 at 20:53
  • There's quite a few thousand Y chromsome SNPs by the looks of it, they're simply under "Y" in my doc. Can't get an exact number because my text document crashes when I try and using the Find function. – Charlie Oct 25 '20 at 21:44
  • Ok, figured it out. My file has 3500 SNPs for the Y chromosome which is slightly more than double what you had from your Ancestry test. Obviously nowhere near what you get from Family Tree DNA (who claim to test 200'000 Y SNPs). – Charlie Oct 25 '20 at 22:01
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A quick Google would have revealed Ancestry currently genotype ~1,700 YDNA SNPs, e.g. Comparing Raw Data from 5 DNA Testing Companies - Fri, 31 Aug 2018. Along with the details of how to convert specific values, in a downloaded data file, into a Haplogroup, eg. SNPedia - Haplogroup Y (Y-DNA)

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