Question: Using gVCF mode in HaplotypeCaller ( GATK4)
gravatar for ahmad mousavi
23 months ago by
ahmad mousavi470
Royan Institute, Tehran, Iran
ahmad mousavi470 wrote:


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?


snp haplotypecaller gatk4 • 2.8k views
ADD COMMENTlink modified 23 months ago by JJ470 • written 23 months ago by ahmad mousavi470
gravatar for andrew.j.skelton73
23 months ago by
andrew.j.skelton735.9k wrote:

You can run Joint genotyping on as little as 2 samples (ASAIK - If anyone has a link to contradict me, please share!), however it's the variant filtering stage that you may have trouble with. In the GATK forums it's recommended that to use VQSR, at least 30 whole exome samples or 1 whole genome sample are needed.

So in your situation of having 3-5 WES samples:

  • Run the haplotype caller in gVCF mode for each sample
  • Consolidate to IntelGenomicsDB (optional step, if you're working with GATK4specifically)
  • JointGenotyping on the resulting gVCF files or IntelGenomicsDB
  • Hard filtering
ADD COMMENTlink written 23 months ago by andrew.j.skelton735.9k
gravatar for JJ
23 months ago by
JJ470 wrote:

Have a look at two previous discussions: C: Joint genotyping using GATK - how important is it? Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?

ADD COMMENTlink written 23 months ago by JJ470
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