REQUIRED for all errors and issues:
a) GATK version used: 4.1.5
b) Exact command used: See below
c) Entire program log: 

Hello Gatk team,

I ran mutect2 on tumor bam file and normal bam file separately: Here is the command used:

#tumor bam file

gatk Mutect2 -R $idx -I ${fn}_markup_primaryonly.bam -tumor ${LB} -O ${fn}_mutect2.vcf.gz

#normal bam file

gatk Mutect2 -R $idx -I ${fn}_markup_primaryonly.bam -tumor ${LB} -O ${fn}_mutect2.vcf.gz

I checked some of the positions in both the vcf files(tumor and normal). They were present in both, so I thought I should filter them as they would be germline variants since normal has it also.
But then I also ran mutect2 as below where I added tumor bam and normal bam in the same command:
gatk Mutect2 -R $idx -I tumor.bam -tumor tumorname -I normal.bam -normal normalbam -O somatic.vcf.gz

My question is, I still see same positions in the somatic.vcf.gz file. I thought since I used normal.bam file, mutect2 will filter out those positions. but that is not happening. Any help is appreciated.

Thanks