Question: Conversion of imputed VCF file to HapMap format
0
gravatar for mab658
15 months ago by
mab65860
mab65860 wrote:

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

snp rna-seq • 2.1k views
ADD COMMENTlink modified 15 months ago by 159932162500 • written 15 months ago by mab65860
1
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

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)
ADD COMMENTlink modified 3 months ago • written 15 months ago by Kevin Blighe56k

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

ADD REPLYlink written 3 months ago by devarora120
1

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

ADD REPLYlink written 3 months ago by Kevin Blighe56k
0
gravatar for 15993216250
15 months ago by
159932162500 wrote:

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

ADD COMMENTlink written 15 months ago by 159932162500

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

ADD REPLYlink written 15 months ago by Kevin Blighe56k
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