Chromosome Y imputation, any good reference panels?

Question

[Floris Brenk]

Hi all,

Is anyone aware of a good reference panel for chromosome Y imputation? I know you could use 1000G, but I am more looking for a larger and more recent reference panel. Like the https://imputationserver.sph.umich.edu/ size..

[lh3]

Except PARs, Y is not recombining. I actually don't think any existing imputation tools work on Y. For Y, what is more important is to find the haplotype group.

[Floris Brenk]

Ok thanks for your reply! As a follow up, are you aware of any tools that can identify the haplotype group based on plink data?

[ruidlpm]

You could use Yhaplo (https://github.com/23andMe/yhaplo) to identify haplogroups in your data. It takes VCF files as input, but if you only have ped files, you can convert them to geno format with convert2genos.py which is provided with the software.