I am new with all NGS tools, I tried to follow best practices workflow for my exome reads from tumor samples: I align with bwa mem, sort with samtools, mark duplicates and recalibrated bases with GATK 4 and finally call variants with Mutect 2. Although the software run successfully I noticed that the mark duplicates metrics only have a 0.3% of duplicates, which I double check with samtools flagstat. So I marked duplicates with samtools, from the same bam, which give a 30% of duplicates.
Later when I did the variant calling the output from the bam mark with samtools was of 297061 mutations againts 50370 from the bam mark with GATK.
I am not sure which file is the right one. What could I be doing wrong? How can I make sure which file is worked correctly?.