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.
Varian quality recalibration annotations.
What annotations are recommended to be used for the variant recalibrator for an exome sequencing project? I am using the Ion proton system so my VCF files are automatically generated after the sequencing run. Also, would I still have to mark duplicates and realign indels in my BAM files before viewing them on a genome viewer like IGV? Since I already have my VCF files, I don't know if this will be necessary.
Thank you, these forums are very helpful!