Mutect2 calls insertion and reverse complement deletion in the same read

Question

[tstem]

Hello everyone,

I'm new with Mutect 2. After analysing two cancer samples from the same patient on hg19 (Tumor and Control), I found strange deletions followed by insertions in my vcfs results files.

In this case I have ,on the same read, an insertion of 8 bps and a few bases after, I have a deletion of the same bases but R/C. I modified my command and add the bamout option.

I can realy see the insertion and deletion in the local realign bam on IGV.

How can we explain this? An error of the variant caller? A biologic explanation?

Many thanks,

Tristan

[Ram]

A few points:

1. Your post is a question about a tool, not an announcement for a new tool. The appropriate post type is Question, not Tool.
2. Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image or the HTML embed code, not the link to the webpage that has the image embedded (which is what you have used here)

I've fixed both issues for you this time, but please be more careful in the future.