Question: Conversion of imputed VCF file to HapMap format
0
gravatar for mab658
2.1 years ago by
mab65880
mab65880 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 • 3.4k views
ADD COMMENTlink modified 2.1 years ago by 159932162500 • written 2.1 years ago by mab65880
1
gravatar for Kevin Blighe
2.1 years ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k 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 13 months ago • written 2.1 years ago by Kevin Blighe69k

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

ADD REPLYlink written 13 months ago by devarora290
1

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

ADD REPLYlink written 13 months ago by Kevin Blighe69k
0
gravatar for 15993216250
2.1 years ago by
159932162500 wrote:

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

ADD COMMENTlink written 2.1 years ago by 159932162500

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

ADD REPLYlink written 2.1 years ago by Kevin Blighe69k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1511 users visited in the last hour
_