Conversion of imputed VCF file to HapMap format

Question

[mab658]

Hi Everyone, I have successfully imputed my VCF file using beagle4.1. How do I convert it to HapMap format, please? Thanks.

Answer 1

[Kevin Blighe]

This could likely be done manually using Shell / AWK commands. However, using pre-existing programs, I would do the following:

1. Convert Beagle output to VCF using Beagle's beagle2vcf.jar
2. Convert VCF to Hapmap format using Tassel's -exportType Hapmap (example at the end, HERE)

[tothepoint]

Dear Kevin, Can we get the updated link for the example? The page is giving error. Thanks

[Kevin Blighe]

Indeed, it seems to have moved. I updated the link.

Answer 2

[15993216250]

Tassel --vcf your file -export file -exportType Hapmap

[Kevin Blighe]

Thank you for just repeating [half of] my same answer.