To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

How GATK deals with Deletions in a repeat region?

gbdaathulgbdaathul IndiaMember
edited January 2016 in Ask the GATK team


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.

Thank you,

Post edited by gbdaathul on


Sign In or Register to comment.