Y Chromosome Haplotype Inference

Question

[Vivek]

Hi,

I'm looking for a command line based tool that can be used to infer the ancestral haplotype from Y chromosome variants. For mtDNA I found a great tool called haplogrep (http://haplogrep.uibk.ac.at/) that does this analysis but I'm unable to find a similar tool for chrY.

If no such tool exists I'm willing to write one and I'd like to know if there is any source that lists the ChrY SNPs by haplotype in a parse-able format. Since I see haplotrees like this:

https://www.familytreedna.com/y-dna-haplotree.aspx

But these are not very parser friendly.

Thanks!

Answer 1

[Leon]

the link maybe help A: Y-DNA and mtDNA Haplogroup Predictor

Answer 2

[Neilfws]

Do any of these links help? - Y-DNA tools.

[Vivek]

Thanks for the link but a majority of these tools are based on Y-STRs instead of SNPs and they are almost all web based. I cannot afford to upload my data.

Answer 3

[julesvanlaar]

Have a look at YBrowse.org