If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
GATK4: ApplyBQSRSpark VS PrintReadsSpark
What is the difference between GATK4 tools ApplyBQSRSpark and PrintReadsSpark?
java -jar GenomeAnalysisTk-4_1.jar PrintReadsSpark -h suggests that output is String as shown below
--output,-O:String uri for the output file: a local file path.
While on the website https://github.com/broadinstitute/gatk output is bam for PrintReadsSpark option as shown below
./gatk-launch PrintReadsSpark -I input.bam -O output.bam
I plan to start testing GATK-4 in coming days. Any thoughts or suggestions will be greatly appreciated.