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.
Hi GATK team,
I was wondering, your best practices for data preprocessing (https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165) don't mention any trimming (using i.e. trim_galore or fastx). It seems like at least some time ago this was pretty standard. Does this mean it is not advised anymore? Can I really take my raw fastq file and map them using BWA directly, without any filtering?