Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Trouble with Best Practices
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?.