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.
gVCFs for Targeted Resequenced data
For targeted re-sequenced data, can we do variant calling using HaplotypeCaller in gVCF mode followed by using GenotypeGVCFs for joint genotyping ?
Would the following best practices work for targeted re-sequencing as well , except for VQSR as for targted resequencing GATK advices another way of filtering.