Constructing a Y chromosome phylogeny from VCF files

Question

[devenvyas]

I have <34 VCF files for the 9.9Mb callable NRY bases per Poznik et al. 2013 (10.1126/science.1237619). (One individual per VCF, some are from women, so they will be omitted)

I want to construct a phylogeny/network to study how they differ. Does anyone have a recommended method/pipeline?

Answer 1

[sankar2004]

First merge VCF files containing data from a single individuals using the VCF Tools (vcf-merge command). Then use the simple one-click software VCF2POPTREE to create a phylogeny from a VCF file containing multiple individuals/strains.