EDIT: to reply to @terdon
We sequence mostly human genome data using Illumina sequencers. As for the type of data, we perform mostly Whole-Exome Sequencing (WES), Whole-Genome Sequencing (WGS).
At the end, after performing all pre-processing, we obtain the VCF files from HaplotypeCaller using GATK. Then we proceed to annotate using VEP.