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 on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

Confusion in using gVCF mode


I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems:

1- Should we run gVCF even when we have one WES sample?

2- I have 3 WES samples, should I use gVCF --> Cosolidate --> GenotypeGVCF --> VCF or it is better to obtain VCF directly from HaplotypeCaller and ignore its next steps?

3- If I have 3-5 WES samples, is it better to run HaplotypeCaller with multiple input (bams) or separately?


Best Answers

  • SheilaSheila admin Broad Institute admin
    Accepted Answer


    If you are sure you will only have 5 samples and never get any more samples to analyze, you can simply run HaplotypeCaller in normal mode. If you think you may add more samples in the near or later future, you should use the GVCF workflow. Have a look at the HaplotypeCaller presentation in the presentations section for more information.


  • Ahmadsam66Ahmadsam66
    Accepted Answer

    Thanks @Sheila , @SkyWarrior for your answers

    DO you suggest to use Haplotypecaller separately for each sample or use multiple input for it?


Sign In or Register to comment.