Heads up:
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.

Running HaplotypeCaller on a multi-lane sample


I am interested in running HaplotypeCaller for a multi-lane sample. What is the best way to do this? I followed the protocol here (https://software.broadinstitute.org/gatk/documentation/article?id=6057) which states to run MarkDuplicates and BQSR before HaplotypeCaller, which I did. I fed the new BAM file into HaplotypeCaller but get an error with a corrupt gVCF file. Am I meant to merge the read groups into a single read group before using HaplotypeCaller?


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