I want to prioritize the functionally relevant somatic variations in cancer normal pairs for which I used Mutect2. Looking at the vcf I found only 10% have passed all the filters and there are many which do not qualify one or more filters defined by Mutect2 as given below:
-alt_allele_in_normal,Description="Evidence seen in the normal sample", -clustered_events,Description="Clustered events observed in the tumor", -clustered_read_position,Description="Evidence for somatic variant clusters near the ends of reads", -germline_risk,Description="Evidence indicates this site is germline, not somatic", -homologous_mapping_event,Description="More than three events were observed in the tumor", -multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal", -panel_of_normals,Description="Seen in at least 2 samples in the panel of normals", -str_contraction,Description="Site filtered due to contraction of short tandem repeat region", -strand_artifact,Description="Evidence for alt allele comes from one read direction only", -t_lod_fstar,Description="Tumor does not meet likelihood threshold", -triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD"
I am not sure among them which are the most important ones and must be considered for calling somatic events and which can be overlooked.
Any suggestions would be highly appreciated. Thanks