We have done Variant calling using Illumina Basespace suite. The vcf file which have been generated was annotated using Variant studio. In the report we came to see a deletion of TA > TA/A . As that region when we viewed in the IGV it shows the picture below(Link).
As in that picture after the T, it is a long repeats of A. The deletions are shown right adjacent A of T. How can we be sure that the deletion happened in that A itself? We think deletion can occur on any other A in that stretch, as the deletion in the report shows the change of TA > TA /A. How the tool predicts it is the adjacent A itself?
Thank you in advance.