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.
When should I use HC in ERC mode?
maybe this is a very basic question but, I've read several posts and sections of GATK Best Practices and tutorials but I can not get the point. What is the main difference between using GATK HC in gVCF mode instead of in multi-sample mode? I know that HC in GVCF mode is used to do variant discovery analysis on cohorts of samples, but what is the meaning of "cohorts of samples"? If I have 2 groups of samples, one WT and the other mutant, should I use GVCF mode? I've read almost all the tutorials and Howto's of GATK and I can not understand at all.
And another question, can I give to HC more than one bam file? Maybe using -I several times? And if I introduce several files, in the raw vcf output file, what I'm going to find? Several columns one per sample?
Thank you in advance.