We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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?.