Tutorial:Y-DNA and mtDNA Haplogroup Predictor

Question

[Shicheng Guo]

Here to introduce some tools to do Y-DNA and mtDNA Haplogroup Predictor

1. https://dna.jameslick.com/mthap/
2. https://ytree.morleydna.com/
3. https://ytree.morleydna.com/extractFromAutosomal
4. http://www.nevgen.org/
5. https://dna.jameslick.com/mthap/

More tools are welcome to share.

Answer 1

[moxu]

I am looking for a good haplogroup classifier using either genotyped information (SNPs) or WGS information (sequencing). Which software products are the most popular (and accurate)?

Thanks!

[Leon]

if you want to use vcf file as software input, for mtDNA, I think haplogrep is the most popular classifier https://github.com/seppinho/haplogrep-cmd.git. However, as I know, there is no available tool to predict Y haplogroup when you provide vcf file containing snps information as input. As a suggestion, you can get haplogroup dict in ISOGG websitehttps://isogg.org/tree/, then write your own scripts to predict Y haplogroup like ypredict-master mentioned above .

[moxu]

Thanks so much for the reply. How about MToolBox?

[Leon]

I have no experience with the method about MToolBox myself.

Answer 2

[Leon]

https://github.com/N-damo/ypredict-master, the software is under development.