This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can only have two alleles(paternal and maternal) that way after variant calling, an allele at one position can be homozygous or heterozygous. So there can be max of two alleles, but why do we see multiple alleles at a given position in VCF. I am trying to understand the science behind this. Please help out. Thanks!
chr5 127640782 . AG A,AA . . . GT:AD:DP 1/2:0,28,409:437
multiple alleles at a given position in VCF.
? Maybe, you could show an extract of a VCF file to show us what you mean. Are you surprised that in the population there can be more than 2 alleles at a given site? $\endgroup$ – Remi.b Sep 28 '18 at 16:34