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.
Confusion in using gVCF mode
I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems:
1- Should we run gVCF even when we have one WES sample?
2- I have 3 WES samples, should I use gVCF --> Cosolidate --> GenotypeGVCF --> VCF or it is better to obtain VCF directly from HaplotypeCaller and ignore its next steps?
3- If I have 3-5 WES samples, is it better to run HaplotypeCaller with multiple input (bams) or separately?