If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
FastQ to VCF - known indels and SNPs VCF files as vcf.gz
I have followed the GATK Best Practices to go from fastQ to VCF files with success thanks to the great documentation you have!
I would like to know if the known indels and SNPs VCF files passed to IndelRealigner and BaseRecalibrator really have to be unzipped or if the tools accept the vcf.gz versions?