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.

Error running haplotypecaller (v3.3)

I am running the haplotypecaller on multiple samples all but one work correctly with the following commands, however one is resulting in a binary file instead of the gvcf. Any suggestions how to fix this?

HaplotypeCaller -i map/30.rmdup.bam -o gvcf/30.gvcf -r reference_F.fasta -p 10 -a gvcf/30.gvcf -g -e hc.log


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