How GATK deals with Deletions in a repeat region?
I just want to know how the GATK calls a deletion of a base in a long repeat region? We came across a situation where GATK called a deletion in a sequence of CTAAAAAAAAAAAG , where TA > TA/A. We viewed it in IGV and came to see that the adjacent A to T have been called as the deletion. We are confused that the deletion can be on any of the A in the repeat, and how the caller predicts it is exactly the adjacent A to T. I am attaching the IGV view also. Please comment on this question.