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Question: How does PLINK --recode12 code SNPs from ACTG to 1 and 2 in .ped files?
0
gravatar for V.S
3.6 years ago by
V.S • 0
V.S • 0 wrote:

I used PLINK --recode12 to transfer my ACTG ped file to 1 2 ped file. But I don't know how PLINK did this recoding, specifically, when should a SNP like A A transferred to 1 1 or 2 2, and also how are the heterozygous ones like A T are coded.

Any help is really appreciated!!
snp genome • 3.3k views
ADD COMMENT • link •
modified 12 months ago by Shicheng Guo • 8.6k • written 3.6 years ago by V.S • 0
4
gravatar for chrchang523
3.6 years ago by
chrchang523 ♦ 7.7k
United States
chrchang523 ♦ 7.7k wrote:

Usually the minor allele is coded as 1 and the major allele is coded as 2.
ADD COMMENT • link written 3.6 years ago by chrchang523 ♦ 7.7k

Thank you chrchang523 !

ADD REPLY • link written 3.5 years ago by V.S • 0
1
gravatar for Shicheng Guo
12 months ago by
Shicheng Guo • 8.6k
Shicheng Guo • 8.6k wrote:

--reference-allele and --recode12 together will be helpful to understand the recoding. Here reference allele will be recoded to 1, the alternative will be 2

plink --bfile input --reference-allele MyReferenceAllele.txt --recode12 --out output

In addition, --reference-allele and --recodeA together will generate additive data for further analysis with R

plink --bfile input  --reference-allele MyReferenceAllele.txt --recodeA --out output
ADD COMMENT • link modified 12 months ago • written 12 months ago by Shicheng Guo • 8.6k
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