Hi, I have some samples from covid cases and normal people. I have already processed and aligned their fastq files to get their variations. I have lineage covid data to compare and contrast with my detected variants as well. As I see in the results, even for some of the normal people there are some variants from delta and omicron lineages.

I would like to change some parameters to somehow prevent reporting such variants for normal people. I am using dragen by illumina for alignemnts and gatk for variants calling.

I would appreciate any help in this case.