Conversion of genotype data: GEN format to matrix with genotypes encoded as 0, 1 or 2
Entering edit mode
6.9 years ago


I am new to GWAS and would appreciate if anyone could help me with my question!

I have an imputed GEN format genotype data. Besides using SNPtest, I am also interested to run the association analysis in R. So, I want to convert the GEN format to a SNPs by sample (individuals) matrix. My question is as follows,

In GEN file each SNP is represented by 3 genotypes (AA, AB or BB) with respective probabilities. Now, in the matrix that I want, I just want the genotype of SNP for each individual. Picking the genotype based on the highest probability is very straightforward. However, if I pick the genotype based on some threshold (for example 0.9) and some SNPs fail to reach the threshold, what to I do in that situation?

I hope my question makes sense! If not I will try to make it clearer1

Thank you!

GWAS SNPtest • 2.1k views
Entering edit mode

I don't know the filtering you want to apply, but if in the given criteria that you set SNP is failing them (meaning not able to correctly assign genotype), I would discard such a SNP


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