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 raws 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.