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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


  • Thanks @Sheila , @SkyWarrior for your answers

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

  • SheilaSheila Broad InstituteMember, Broadie, Moderator


    If you choose to run the GVCF workflow, you will have to run on each sample separately. If you run HaplotypeCaller in normal mode on all samples, you can run with all BAMs at once. Have a look at this article as well.


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