We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
HaplotypeCaller 4.beta.6 gVCF performance
Hi, ever since the 4.beta.4 release, I've noticed a significant increase in the memory requirements and execution time of HaplotypeCaller in gVCF mode. I tested the 4.beta.2 and 4.beta.6 version of HaplotypeCaller with a NA12878 BAM, aligned with BWA 0.7.13 with approximately 30x coverage. 4.beta.2 completed after roughly 5h with 2GB of memory, while 4.beta.6 completed after roughly 30h with 15GB of memory. 4.beta.6 failed with an out of memory exception when given less memory.
Both versions were ran with the same settings (--interval_set_rule UNION --genotyping_mode DISCOVERY --createOutputVariantIndex --emitRefConfidence GVCF) and parallelized on intervals from a custom BED file.
From my understanding of the release notes, the versions from 4.beta.4 onwards have a bug fix that corrects the results of HaplotypeCaller in gVCF mode. Is the performance difference to be expected?