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.
Can GenotypeGVCFs be ran without filtering?
For bacteria genomes I use the "Best Practices" and the HaplotypeCaller to call variants. I would like to output a VCF containing all positions I can then parse on my own. I'm using -ERC BP_RESOLUTION to output such a VCF. However to get INFO such as AC and MQ I need to follow up with GenotypeGVFs, and there doesn't seem to be an option to keep all positions when using this. In the end I must have a VCF which contains all possible variants and any position with zero coverage. Is there a way to generate a VCF with every reference position that includes AC and MQ values.