I'm new with GATK. I usually use Varscan for variant calling with the following options :
--min-coverage 7 --min-reads2 7 --min-var-freq 0.80 --variants
Which options I have to use with Gatk 4 HaplotypeCaller for similar results?
Please read the HaplotypeCaller tool document at https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php. The available arguments are summarized in a table under HaplotypeCaller specific arguments. Clicking on one of these will take you further down the document to a more detailed explanation.