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.

Converting FASTQ to BAM

I'm trying to convert FASTQ to BAM file using FastqToSam and I'm using the following syntax:

java -jar Downloads/picard.jar FastqToSam \ FASTQ=Path/filename.fastq.gz \
OUTPUT=Path/filename.bam \

I keep getting the error message "FASTQ is not recognized as an internal or external command, operable program, or batch file"

I apologize if this is an obvious issue.


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