How To Revert Allele Data To Atgc With Plink After Recoding To 12 Format

Question

[kumar.vinod81]

I've recoded my SNP data in --recode12 format using PLINK. Now I want to recode back to my data in ATGC data. What will be the update allele codes?

[zx8754]

"I've recoded my SNP data in --recode12 format using PLINK" Then you must have original MAP file with ATGC alleles?

Answer 1

[NB]

To recode SNP alleles from A,C,G,T to 1,2,3,4 or vice versa, use --allele1234 (to go from letters to numbers) and --alleleACGT (to go from numbers to letters). These flags should be used in conjunction with a data generation command (e.g. --make-bed), or any other analysis or summary statistic option.

[NB]

Well, I am not too sure then, maybe try this - you need a text file which has the original ATGC alleles

A A  1 1
A C  0 0
A C  1 2
C C  1 2

and then create a file for the --update-allele comand in this format

SNP identifier
Old allele code for one allele
Old allele code for other allele
New allele code for first allele
New allele code for other allele

For example,

   1 1   A A
   1 2   A C
   ...

will change allele 1 to A and allele 2 to C for , etc.

[kumar.vinod81]

Mean I am to give a list for all of 6000 SNPs. Its I think impossible. Thanks

[NB]

If you can code a little with perl or shell scripting, it is not impossible.