I'm trying to play around with my family's raw genetic data from Ancestry.com so that I can do some genetic analyses, and I noticed in the AncestryDNA raw data files that some regions of the genome have more than one variant associated with them and I would like to know why this is. The end goal is get this into a regularly formatted VCF, but I feel that these double variants will probably mess things up. So for example one might see something similar to this in the tab-delimited file:
rs6010164 22 50515270 T T rs267607236 22 50515270 I I
(Header line: rsid chromosome position allele1 allele2)
I understand that when rsid numbers were created, sometimes multiple rsid numbers were accidentally assigned to the same region of the genome, but I do not understand how two separate variants can be assigned to one single region in the genome. I could be wrong but as I understand it, I should only see one line here (either a "T T" or an "I I") because genotypes are reported in comparison to the human reference genome and so each position should uniquely refer to a single nucleotide in the said human reference genome.
But in this example case one line says there is a "T T" genotype at this position, and the other line says there is an insertion(see "How do I read my raw DNA data?" here). One possible explanation I thought of is if this would just be saying that a T was inserted, but if this is the case, then as I understand it the reference allele present in the individual should still reported, just in conjunction with the allele at the index. (So assuming an extra "A" was inserted after the T, which could be the reference or alternative allele, something like this should be recorded: rs6010164 22 50515270 TA TA).
Can anyone help me understand why there are two separate variants associated with chromosomal position? Thanks!