PLINK Reference haplotype for Odd Ratio calculation

Question

[cobraimovic]

Hi,

I have a simple PED/MAP file composed by ~900 individuals genotyped for 2 SNPs.

I performed a conditional haplotype test with the following command:

plink --file dataset.ped --chap --hap-snps rs1-rs2 --ci 0.95 --out results

The program give this type of results:

  HAPLO         FREQ                        OR(A)                        OR(N) 
-------       ------      -----------------------      ----------------------- 
     GA       0.0451                 (-ref-)                      (-ref-) 
     CA        0.319        0.6187 (0.331; 1.16 )                         |    
     GG        0.304             1.606 (0.86; 3 )                         |    
     CG        0.331        0.5945 (0.334; 1.06 )                         |    
-------       ------      -----------------------      -----------------------

As explained in the plink manual, the OR (Odd Ratio) is calculated using a reference haplotype picked randomly which is the "GA" in this case.

I was wondering if there is a way to change the reference haplotype because I would like to put as reference the "CA" haplotype, which is the most common in human population checking the literature.

Thank you

[Oskar]

Dear cobraimovic - I had the same issue. Nevertheless, I figured it out that if you run the following command, you will get the information for "CA" haplotype as the reference haplotype under the Null model

plink --file dataset.ped --chap --hap-snps rs1-rs2 --ci 0.95 --control GA,GG,CG --out results

Hope it helps.

Answer 1

[muzilijiao]

hi, have you already know how to change the reference haplotype?