Most of mapped reads are disappeared after Mutect2

Hi, I'm HJ.Kwon.

I found some strange result from Mutect2 run.
I'm analyzing Breast Cancer FFPE sample for research.

In final vcf file, I couldn't find ERBB4's mutation which is already confirmed by Tumor+Normal run.
So, I made bamout bam and compared it with original bam files through IGV.

In the IGV, I found all the reads mapped to ERBB4 are disappeared.
And, the same thing happened to PIK3CA except it has one region has remained.

I'm attaching two IGV screenshots.
All MAPQ values is higher than 40 in the original bam file.
Is a bamout bam file is the final bam file to call the variants, isn't it?
Then, I want to know how's bamout bam is generated, and I wonder if I can adjust some parameter not to lose many reads?

1. PIK3CA (upper part is bamout.bam)

2. ERBB4