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.
...you did not provide enough memory to run this program,pooled,haplotypecaller
I am using haplotypecaller version 3.4-46 with pooled data (ploidy 44) and I am running in to the error 'There was a failure because you did not provide enough memory to run this program'. I have a very high coverage (~10000x at each position). Searching in the forums, I have found suggestions of down sampling, (which haplotypecaller does itself in the version I am using) and changing the minPruning parameter (which I am afraid may further compromise the sensitivity of the variant calling given the samples are pooled). Previously I used unifiedgenotyper on the same data and I had no problems. Is there something else I could try to get rid of the memory issues or should I stick with unifiedgenotyper in my case? Thank you for your support.