How to get allele coding

Question

[LZhang]

Dear All:

I am new to bioinformatics. Recently I got genotyping files from PLINK, and need to transfer these SNP to either 0/1/2 or Illumina AA/AB/BB format.

For each sample, I have the snp file format (19 columns, and ~10k rows for SNP position for each sample):

SNP_Name   Allele1_Forward    Allele2_Forward   Chr    Position    Allele1_Top    Allele2_Top    Allele1_Design    Allele2_Design    Allele1_AB    Allele2_AB    Allele1_Plus    Allele2_Plus   SNP    ILMN_Strand    Customer_Strand    Top_Genomic_Sequence    Plus/Minus_Strand SNP_Index
exm106217     T    T      1    155205634   A    A    T    T    A    A    -    -    [T/C]    BOT    BOT     -  TOP     10
..

From on above file, I extract columns 1, 14, 15 16, (exm106217 [T/C] BOT BOT), I have PLINK bim file, like:

1    exm106217    0    155205634    C    T

How can I get the allele coding information (0/1/2 or AA/AB/BB) in this position based on these two files (bim file and snp file )? I have tried to Gengen package without success.

Any package or command I can use to transfer all SNP position to allele coding?

Thanks for your help.

Answer 1

[akang]

Hey LZhang! You can recode in PLINK itself with the --recode12 option