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.
GATK v188.8.131.52 HaplotypeCaller
I am using GATK v184.108.40.206 HaplotypeCaller for variant analysis. (paired-end DNA sequenced data mapped to the reference using BWA mem).
The command I used;
“gatk HaplotypeCaller –R Reference.fna –I input.bam –O output.vcf”
It runs for a while (couple of seconds) but does not produce an output. No error message was given. Am I doing this right? Any help is appreciated.