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.
GATK Input as list of BAMs
The GATK documentation states the -I arguement can be List[String], which when using HaplotypeCaller or UnifiedGenotyper would produce a multisample vcf.
However, I am confused as to how exactly I present my list of bam files. Is there a way to pass in t
he name of a text file which contains a list of many bam files, something like