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.
Variant Annotator and other CALLERS
talking about VariantAnnotator, could it be safely used on VCF files produced by other callers like STRELKA, VIRMID, Varscan2 etc ...beside MUTECT1 or MUTECT2 ? I am referring to the use of VariantAnnotator with the options for FS, SOR, RMSMappingQuality, QualByDepth, ReadPosRankSumTest ...
or, are there any minimal requirements for a VCF file produced by other callers in order to be fully annotated by VariantAnnotator ?