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!!
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written
by
V.S •
2 answers
Usually the minor allele is coded as 1 and the major allele is coded as 2.
--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
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