Association study

[scami]

Dear all,

I have a locus of around 4000bp and I know that this locus is involved in showing a certain phenotype, lets call it phenotypeA.
I have resequenced 8 organisms of the same species, 4 with a 4 without phenotypeA. I aligned the reads on the locus and have snps and indel for all of them with the relative homozigosity level. Now I would like to know which are the snp or indel that differentiate the two phenotipic groups in order to understand which polymorphysm the phenotype rely on.
Any suggestion on how to do this?
thanks!

[dpryan]

This sounds like a classic case for logistic regression.

[scami]

Thanks!

I am not a great expert of this statistical test but I will have a look at it. Any further suggestions will be appreciated.

[narain]

SEND ME THE DATA, I WILL DO THE LOGISTIC REGRESSION FOR YOU. You can also try CHAID.

[SNPsaurus]

Wouldn't all or nearly all the SNPs behave the same way in a 4 kb region? It depends on the LD block length for your species, of course. Do you believe the trait phenotype depends on a single gene? If it does, then just list the SNPs and look for the ones that have one allele in one population and the other in the other population (or homozygous vs heterozygous, depending on dominant or recessive). If it isn't a simple one allele to one phenotype situation, then your sample size is far too small.