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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
How to run Queue end-to-end starting from FASTQ files
Queue purports to offer users a seamless pipelined integration of BWA, Picard and GATK. Yet Queue requires BAM files as input, implying I would need to call BWA separately to do alignment and then Picard or samtools to convert to BAM, then go back to Queue to work with the BAMs. At this point I run into compatibility issues for instance as described here. So is there a way I can set Queue to take FASTQ files as input?