I have used GATK's pipeline (RNA-seq alignment) and obtained a VCF file using Mutect2 and FilterMutectCalls. Filters such as PASS, Clustered_events, germline, weak-evidence, etc. were added to the variants. Before annotating the file with dbSNP, COSMIC, ANNOVAR, I would like to filter out significant somatic mutations into a separate file in order to facilitate easier analysis. Is it a good practice to exclude all the variants whose filter is not 'PASS'? Also, in case of deciding whether the variant is germline, is the presence of 'germline' filter alone sufficient or it is better to set a threshold to the GERMQ score?
Or is it better to filter out variants after annotating the files?