Multiple SNP genotyping to determine a phenotype

[aresx]

Hi all,

Currently, I have a genotype database containing several SNPs with genotype and allele frequency, and phenotypes.
I'd like to call these SNPs of the sample and determine the possible phenotype upon the database.
Does anybody know what tool I can use or what algorithm I can apply using the information of genotype and allele frequency, and phenotypes?
Thanks a lot in advance.

[Heisman]

It's not completely clear to me what you are asking. Could you give an example of your genotype database (like a few lines of it), as well as your phenotype information? Do you have raw read files for a sample from which you need to call SNPs?

[aresx]

It's not completely clear to me what you are asking. Could you give an example of your genotype database (like a few lines of it), as well as your phenotype information? Do you have raw read files for a sample from which you need to call SNPs?

Thanks for your reply.

I have the database as follows.

ID Genotype1 Genotype2 Genotype3 Freq1 Freq2 Freq3 Pheno1 Pheno2 Pheno3
rs00001 AA AT TT 0.034 0.736 0.23 Abnormal1 Normal Normal
rs00002 CC CA AA 0.487 0.094 0.419 Normal Abnormal2 Normal

If I have genotyping results as below,
SampleA
rs00001 AA
rs00002 AA
SampleB
rs00001 AA
rs00002 CA

how do I determine phenotype with possibility for SampleA and B?

Thank you.

[swbarnes2]

You can't determine a phenotype computationally!

At best, you could do a t-test or ANOVA, or something like that, and see associations between genotype and phenotype, but you can't be sure that you can really predict a phenotype based on a genotype. Not without hard biological studies showing a mechanism.