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.
Question about joint calling
I have a question regarding types of reads in bam files in joint calling. That is, can we do joint calling using both single-end and paired-end mapped reads as input files? Or should we stick to only one type, single end or pared end for consistency and technical reasons?