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.
skipping MarkDuplicates in deep sequencing data
Hi GATK team,
Recently I have been working with deep sequencing data(target capture data,about 200x depth,BAM file was sorted ,about 3.39G size),but I was stucked in Picard MarkDuplicates , it took 85h so far and I expect it will takes more time. So can I skip MarkDuplicates and I want to know if skipping MarkDuplicates would result in some big effects in somatic mutation calling with MuTect?