How to convert genotypes "1, 2" to "0,1, 2"?

Question

[Emy]

Hi everyone,

I have genotypes with the codes of 1 and 2. For my aim, I must convert them to 0, 1, and 2. I found that plink can do it. So, I run them by plink with the use of the below codes.

shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --horse --recode --out rk")
3011 3011 2788 2327 1 1.4625 2 2 1 1 1 2 2 2 1 2 1 1 2 2 2 1 1 2 1 2 1 1 2 

shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --horse --recodeA --out rA")
3011    3011    2788    2327    1   1.4625  0   0   1   0   1   0   0   1   1   1   0   1   1   1   1   1   1   1   1   1

shell("plink --file r --maf 0.05 --geno 0.01 --mind 0.1 --hwe 1e-6 --nonfounders --horse --recodeAD --out rAD")
3011 3011 2788 2327 1 1.4625 0 0 0 0 1 1 0 0 1 1 0 0 0 0 1 1 1 1 1 1 0 0 1

By the use of --recode, I only see 1 and 2 codes. For --recodeA and --recodeAD options, they generated codes 0, 1, 2. But when I compared the results of them, they are different in genomic regions.

How can I have accurately converted genotypes (0,1,2) from my data? Which option in plink is suitable for my work?

Thanks

Answer 1

[Kevin Blighe]

Using just --recodeA is the usual way to do this, as per: convert from plink format into 012 format

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For "--recodeA" and "--recodeAD" options, they generated codes 0, 1, 2. But when I compared the results of them, they are different in genomic regions.

You should not directly compare the results of these - they produce different results. Please see:

• https://www.cog-genomics.org/plink/1.9/data#recode

Or, please explain what you mean by "they are different in genomic regions"

Kevin

[karthivalarmathi99]

why important snps remove in --geno 0.2 filter steps ? i have gwas study in plink but remove important snps in alzheimer disease ( rs429358) --geno step. pls explain Kevin Blighe