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?