I have hapmap or Plink format.
I want genotype binary -1/0/1 convert
I want to create an input file in BGLR or BWGS to use gBLUP. If you have an R package or any other good method, I'd love to hear your advice!
You can first convert the "ATCG" hapmap format of your file to numerical genotypes format in TASSEL. Then simply write an appropriate R scrip to convert into the -1/0/1.
For example, here is how I convert my file from the 0/1/2 to 1/0/-1
file[file== "0"]< - -1
file[file== "1"]
Thank you Admas Alemu. I found out how to change it to -1/0/1 at https://github.com/haktansuren/snp-toolset.
I opened SNP_HapMapToNumeric.pl and found that changing -1/0/1 for hetero and homo changed.
Thanks for your reply.
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