Question: Genotypes conversion (Affymetrix chip)
1
gravatar for clarissa.boschiero
3.7 years ago by
Brazil
clarissa.boschiero20 wrote:

Hi all, I am have one file with genotype info from many individuals, for example (file 1)

    SNP1     1       1       1       1       1       1       0       1       0       1  

   SNP2     2       2       2       2       2       1       1       2       2       1     

I have another file with the information of alleles of each SNP, as example (map file):

    SNP_ID  Chr     Pos     Alele_A/Alele_B

    SNP1     17      306961  T/C

    SNP2     1       72709827        A/G

How can I to convert file 1 to their respective genotypes (from file 2)?

Information important:

  • -1= no call
  • 0=AA (homozygous for the reference allele)
  • 1=AB
  • 2=BB (homozygous for the alternative allele)

thanks

Clarissa

snp genotype chip • 1.5k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by clarissa.boschiero20

You can either use plink --recode option or use awk or sed (Example : sed 's/1/AB/g' inputfilename > outputfilename).

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by akang90
1
gravatar for clarissa.boschiero
3.7 years ago by
Brazil
clarissa.boschiero20 wrote:

The code is:

  • -1= no call
  • 0=AA (homozygous for the reference allele)
  • 1=AB
  • 2=BB (homozygous for the alternative allele)
ADD COMMENTlink written 3.7 years ago by clarissa.boschiero20

Gotta love it when folks answer their own questions--really helpful for the rest of the community!

ADD REPLYlink written 3.7 years ago by Sean Davis25k

So sorry it was my first question here. I wanted to add some important info, but the correct is to edit the question. Can I delete my reply?

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by clarissa.boschiero20
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