MuTect2 Discards lots of reads?

MuTect2 discards 74.26% of the reads as below, becasue of 39% duplicate reads ans 34 % notprimary reads.Below is Star alignments we have higher mapping? And below is my commad, I don't have matched normal tumor so I compare tumor to PON::

Command

 s76mutect2.vcf.gz: 
        java -jar ${GATK}/GenomeAnalysisTK.jar -T MuTect2 \
        -I:tumor s76.bam \
        --dbsnp ${DBSNP} \
       --cosmic ${COSMIC} \
       --normal_panel pon_siteonly.vcf.gz \
       --output_mode EMIT_VARIANTS_ONLY \
       -o s76mutect2.vcf.gz \
       -R ${hg38}.fasta

MuTect2

INFO  15:51:22,661 MicroScheduler - 95548100 reads were filtered out during the traversal out of approximately 
128672300 total reads (74.26%) 
INFO  15:51:22,663 MicroScheduler -   -> 5587 reads (0.00% of total) failing BadCigarFilter 
INFO  15:51:22,664 MicroScheduler -   -> 51034583 reads (39.66% of total) failing DuplicateReadFilter 
INFO  15:51:22,679 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
INFO  15:51:22,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  15:51:22,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO  15:51:22,684 MicroScheduler -   -> 44507930 reads (34.59% of total) failing NotPrimaryAlignmentFilter 
INFO  15:51:22,685 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
------------------------------------------------------------------------------------------
Done

STAR

                      Number of input reads |       33174546
                  Average input read length |       270
                                UNIQUE READS:
               Uniquely mapped reads number |       25779436
                    Uniquely mapped reads % |       77.71%
                      Average mapped length |       272.83
                   Number of splices: Total |       11186136
        Number of splices: Annotated (sjdb) |       0
                   Number of splices: GT/AG |       11038925
                   Number of splices: GC/AG |       67204
                   Number of splices: AT/AC |       5902
           Number of splices: Non-canonical |       74105
                  Mismatch rate per base, % |       0.47%
                     Deletion rate per base |       0.02%
                    Deletion average length |       1.34
                    Insertion rate per base |       0.01%
                   Insertion average length |       1.60
                         MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |       6200684
         % of reads mapped to multiple loci |       18.69%
    Number of reads mapped to too many loci |       277368
         % of reads mapped to too many loci |       0.84%
                              UNMAPPED READS:
   % of reads unmapped: too many mismatches |       0.00%
             % of reads unmapped: too short |       2.62%
                 % of reads unmapped: other |       0.15%
                              CHIMERIC READS:
                   Number of chimeric reads |       0
                        % of chimeric reads |       0.00%

Thanks