Hi Rupesh

You can use the plink "recode" commands such as below:

plink (or ./plink in Unix based OS) --file data (ped and map or tped and tfam) --recodeA --"organism, if is not human (e.g. --sheep)"

output If C is the minor allele :

SNP SNP_A

AA 0

AC 1

CC 2

00 NA

hope to be helpful.

Mehdi Esmaeilifard Thank you for your comment but I have accessions that having genotyping data as AA, CC, TT, GG as they are not biparental they are homozygous individual lines. In this case, what should I do?

Dear Rupesh,

I'm not familiar with this kind of SNP data. If I'm not mistaken, this type of SNPs is used more frequently in plant breeding and also in human disease studies. Due to a lack of variation in your SNP data, I think you can not use this data as is common in studies such as GWAS. Please Google this: "SNP-array based whole genome homozygosity mapping", I think you can find some good paper and make some connections.

I hope to be helpful and correct. Sorry for not being able to help more.

Mehdi Esmaeilifard Yes you correct. I am working on soybean. I will try some other way to resolve this. Thank you for your suggestions.

Below R code would do it all, just feed in your snp data in hmp format and prior running the code install required R packages such as rrBLUP. The resulting numeric file will be saved as "snp_data_numeric.txt" in respective directory.

create_phenotypes(

geno_file = "snp_data.hmp.txt",

add_QTN_num = 3,

add_effect = 0.2,

rep = 10,

h2 = 0.7,

out_geno = "numeric",

model = "A",

output_dir = "numericalization",

home_dir = getwd())

Dear Sandeep, Thank you very much for suggestion. I have resolved that issue long back.