Question: Using gVCF mode in HaplotypeCaller ( GATK4)
gravatar for ahmad mousavi
14 months ago by
ahmad mousavi410
Royan Institute, Tehran, Iran
ahmad mousavi410 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 • 1.9k views
ADD COMMENTlink modified 14 months ago by JJ430 • written 14 months ago by ahmad mousavi410
gravatar for andrew.j.skelton73
14 months ago by
andrew.j.skelton735.6k 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 14 months ago by andrew.j.skelton735.6k
gravatar for JJ
14 months ago by
JJ430 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 14 months ago by JJ430
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1524 users visited in the last hour