Let's say I'm sequencing a donor, and I have 20X coverage. And let's say all the reads covering a particular base has the same allele at the position. Then, is that position considered a "variant" with only 1 allele in that position or is that not even considered a variant?
The reason I'm asking is, I was given some read data, and it's in the form location:variant - location:variant.
But there was often the case where for all the variants at a particular location, there was only one allele. But this data is labelled to only have variants. Hence, how is a particular location deemed a "variant."
For example, lets say I'm told that the following is "variant reads given in the form read# location:variant - location:variant"
read 1 6523432: A - 6710432 T read 2 6523432: C - 6710432 G read 3 6523432: A - 6710432 T read 4 6523432: C - 6710432 G
Then, why are these two locations considered variants? It seems like it's just a heterozygous locations. Why were these locations considered to carry variants? Similarly,
read 1 6523432: A - 6710432 T read 2 6523432: A - 6710432 T read 3 6523432: A - 6710432 T read 4 6523432: A - 6710432 T
In those reads, it just seems like it's homozygous. Why is it being called a variant? How was it classified as such?
Put another way, if I'm given 100000 reads, and I said I only want to look at informative reads, and so I'm given a subset with only 100 reads, and those 100 reads look something like the above, then how were these reads selected?