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.
Changing GATK base quality score input
I am working with low quality data from a non-model organism. The average base quality in my reads is about 28. Are there any flags in GATK4 (or GATK3) that will lower the base quality threshold so that GATK assigns higher GQ values to these bases?