Using gVCF mode in HaplotypeCaller ( GATK4)

Question

[ahmad mousavi]

Hi

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?

Thanks.

Answer 1

[andrew.j.skelton73]

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

Answer 2

[JJ]

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?