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Conversion of imputed VCF file to HapMap format

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

rna-seq snp
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updated by 15993216250 • 15993216250 • written by mab658 mab658

2 answers

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)
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written by Kevin Blighe Kevin Blighe

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

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written by tothepoint tothepoint

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

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written by Kevin Blighe Kevin Blighe

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

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written by 15993216250 • 15993216250

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

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written by Kevin Blighe Kevin Blighe

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