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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.

The .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?

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  • $\begingroup$ Based on sciencedaily.com/terms/allele.htm, each gene can be represented by a set of alleles, and alleles are just alternative forms of a particular single-nucleotide sequence; and since they can posses 2 different forms for the given genome (resulting in a 3 distinctive combinations), they are called SNPs. Besides alleles, there are also other in-between single-nucleotides in the gene, but these are the same for the whole population of a given (e.g. human) genome. True? $\endgroup$ – user2340939 Feb 17 at 19:48
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From what I could find the .gen file format for SNPs was developed for the IMPUTE2 program and is generally meant to be a flexible file format for SNP data. The description of the file format is supposed to documented here (multiple pages pointing to that link), sadly that link is broken / the site is removed. However, I found some other descriptions of the format:

In the GEN format each SNP is represented as a set of three probabilities which correspond to the allele pairs AA,AB,BB.

from here

The genfile contains predictor values, one row per predictor.
--gen-skip indicates how many header rows (typically 0 or 1);
--gen-headers indicates how many header columns (typically 0 to 5).
--gen-probs should be 0, 1, 2, 3 or 4:
0 - haplotypes - predictor values should be "0 0", "0 1", "1 0" or "1 1"
1 - dosages - predictors provide the (expected) number of A alleles
2 - two probs - providing probability of being AA or AB
3 - three probs - providing probabilities of being AA, AB or BB
4 - four probs - providing probabilties of being AA, AB, BB or NA, where A and B are the A1 and A2 alleles

from here

Like finswimmer already wrote in his answer, it is very important to be clear about what is considered an allele in the context of SNPs. For the .gen file format this is the identity of the base at a given (SNP) position and since humans have a diploid genome, the allele of a specific individual can be one of three versions (usually called AA, AB & BB).

Regarding your specific points:

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?

  • The alleles in the .gen file refer to the respective SNPs not genes.
  • There is no reason to assume that an given .gen file only contains certain SNPs; if it does this is not due to the data format.
  • The SNPs in a .gen file do not generally have to be linked to a gene.
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The definition of allele depends on the context.

If you look at the DNA of a single person you have usually two copies of each autosomal chromosomes. Each copy is called an allele. If you know look at the sequence at a specific position, you can say one of the two bases are located at one allele and the other base on the other allele.

Beside this there is a definition of allele if you take a look at a many persons or a whole population. Here you call an allele "as alternative forms of a particular sequence".

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