I have a few questions I can't seem to get a straight answer to, regarding the
.gen file format and also biology in general.
.gen file format specifies SNPs for individuals.
Since each SNP has associated allele A and allele B, I assume that the file only contains Causative SNPs, and not Linked SNPs, since the former reside in the gene, and the later don't. Since each SNP in the file has an associated gene (actually genotype, some combination of allele A and B). Correct?
SNP indicate a single position in genome, so why can allele be identified with a sequence larger then one? Or does it indicate just a starting point, where each allele can be of different length, which can be greater than 1?
Allele should be a particular variant of a specific gene, but in other places I saw the definition "Alleles are alternative forms of a particular sequence.". The later seems more logical, if looking at the
.gen file, but it's contradictory to the first statement. So, what's the correct definition?