PLINK Reference haplotype for Odd Ratio calculation
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
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cobraimovic •
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cobraimovic •
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hi, have you already know how to change the reference haplotype?
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muzilijiao •
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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.