Once I Got The Snparray Genotyped , What'S The Next Step

Question

[edufoju]

I just genotyped an SNP array from .CEL file using the R package "crlmm", now I have a variable called crlmmResult, which is the .CEL file genotyped ( a big file with samples and the SNPs genotype (1, 2 or 3).

Can someone help me in what is the next step for processing the SNP array (which R packages to use)? If I want to know what SNPs are related to disease for example.

Also I don't understand exactly what the genotype mean in SNP, AA means no change and BB means there's a SNP?

Thanks.

Answer 1

[Devon Ryan]

Since you already have everything in R, you might try the R interface to the Ensembl Variant Effect Predictor, which will give you much of the information you're after. Regarding the genotyping, AA is usually homozygous for the reference, whereas BB would be homozygous for the variant (there can, of course, be more than one variant).

[edufoju]

I think this is the package I am searching for, thank you!. But how I convert the .CEL file to .VCF, which is the file I need to input to the package.

[Devon Ryan]

Presumably there's a convenient way to convert the genotype calls to a VCF. From googling around a bit, it looks like you can at least make .ped and .map files (for plink), which can be converted to VCF. I suspect there's a better way to do that, but I'm not familiar with the crlmm package.

Having said that, since you're using an array (and therefore not looking for new mutations), you might consider the GWAS approach outlined in the link in neilfws' reply.

Answer 2

[Neilfws]

The next step is to read all of the crlmm documentation. It seems that you have read the genotyping vignette. Next, try the downstream analysis vignette, which explains the basics of conversion to a SNPset for GWAS.