This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Y Chromosome Haplotype Inference

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!

haplotype
• 4,041 views • link
updated by Leon Leon • written by Vivek Vivek

3 answers

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

• 0 views • link
written by Leon Leon

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

• 0 views • link
written by Neilfws Neilfws

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.

• 0 views • link
written by Vivek Vivek

Have a look at YBrowse.org

• 1 views • link
written by julesvanlaar • julesvanlaar

Log in to answer this question.

More posts like this