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 discovery starting from gVCF file
Hello, as the title suggests I'm looking to use the variant discovery tools, specifically SNP discovery. However I am not starting with a FASTA or BAM file, indeed I do not currently have access to them, instead I'm starting with a gVCF file that many of the relevant commands such as haplotype caller do not accept gVCFs as input, and for those commands that do use gVCFs it is implied that they should have been produced by haplotype caller.