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!
Single-Sample Genotyping: Different Workflow?
If I need to independently call and genotype a single sample, is there a different workflow or set of GATK tools and settings that I ought to use instead of using haplotypecaller to generate a GVCF and then using genotypegvcfs to genotype a "batch of 1"?
(In other words, is there another tool or setting that will go directly from BAM to VCF and give better or significantly different results than above.)
I'm aware of the many benefits of the GATK best practices workflow for singly-calling BAMs to GVCFs and then jointly genotyping the batches; however, at the moment I am doing some benchmarking for a project where a joint-calling pipeline may not be feasible and we may need to call each sample independently.