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.
Dynamically pass multiple input to Picard's MarkDuplicates (multiplexed data)
To pass multiple BAM files to
MarkDuplicates we use the following syntax:
java -jar picard.jar MarkDuplicates \ INPUT=lane1.bam \ INPUT=lane2.bam \ OUTPUT=dedup.bam \ METRICS_FILE=dedub_metrics.txt
However, this syntax doesn't requires us to know the number of inputs beforehand. This is not particularly practical. Is there no way this can be done dynamically, for example, some GATK functions take files containing a list of input files (but