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.S0
V.S0 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 COMMENTlink modified 12 months ago by Shicheng Guo8.6k • written 3.6 years ago by V.S0
4
gravatar for chrchang523
3.6 years ago by
chrchang5237.7k
United States
chrchang5237.7k wrote:

Usually the minor allele is coded as 1 and the major allele is coded as 2.

ADD COMMENTlink written 3.6 years ago by chrchang5237.7k

Thank you chrchang523 !

ADD REPLYlink written 3.5 years ago by V.S0
1
gravatar for Shicheng Guo
12 months ago by
Shicheng Guo8.6k
Shicheng Guo8.6k 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 COMMENTlink modified 12 months ago • written 12 months ago by Shicheng Guo8.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1611 users visited in the last hour
_