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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 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.


  • Accepted Answer

    Thanks @Sheila , @SkyWarrior for your answers

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


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