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Haplotype Vs Multilocus Test

Hello!

I've been looking at association tests for groups (2 or 3) SNPs. Is there a difference between haplotypic and multi-locus association test ? The haplotypes I am referring are not the ones in LD, but rather, a combination of alleles from different SNPs in the same gene. Plink has an option for haplotypic test, but does anyone know if it is possible or necessary to phase haplotypes in population studies with data from limited SNPs (~50)? Additionally, do you know of any other software which can provide omnibus results for QT analysis?

Many thanks, Varun

haplotype plink association
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updated by zx8754 zx8754 • written by Varun • Varun

1 answer

To test if SNPs have an independent effect, see "Covariates and interactions" section, you can use SNP or SNPs as covar

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written by zx8754 zx8754

Thanks! I'll give that a try!

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written by Varun • Varun

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