Question: How to get allele coding
gravatar for LZhang
5.6 years ago by
United States
LZhang0 wrote:

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 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.


snp • 2.4k views
ADD COMMENTlink modified 5.3 years ago by akang90 • written 5.6 years ago by LZhang0
gravatar for akang
5.3 years ago by
akang90 wrote:

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

ADD COMMENTlink written 5.3 years ago by akang90
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