I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please?
This could likely be done manually using Shell / AWK commands. However, using pre-existing programs, I would do the following:
Can we get the updated link for the example? The page is giving error.
Indeed, it seems to have moved. I updated the link.
Tassel --vcf your file -export file -exportType Hapmap
Thank you for just repeating [half of] my same answer.