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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!
How to combine the interval after GenomicsDBImport
I am trying to build a GenomicsDB database using GenomicsDBImport on 6000 samples. Running on all chromosomes in one go seems to tage many weeks of processing time. If I use small intervals, how do I then combine the different GenomicsDB foldes afterwards? Or is there a different strategy?
I use GATK 4.1.1 and this is my command with all chromosomes that takes forever
gatk --java-options "-Xmx4g -Xms4g" \
--genomicsdb-workspace-path genomicsdb \
--batch-size 50 \
-L all_chromosomes.bed \
--sample-name-map sample_map \