Hello everyone 

MuTect2 from GATK3 discarded `87.33%` of the reads.  This is during preparing panel of normals. 
I will use sp1.vcf in the PON creation !

    sp1.vcf: sp1.bam
            java -jar ${GATK}/GenomeAnalysisTK.jar \
            -T MuTect2 \
            -R ${hg38}.fasta \
            -I:tumor sp1.bam \
            --dbsnp ${DBSNP} \
            --cosmic ${COSMIC} \
            --artifact_detection_mode \
            -o sp1.vcf
     

**Does this seem okay to you? Is there anything I can do to fix non primary reads `(42.77%)` and duplicate reads `(44.56%)`?**


    INFO  00:57:17,188 MicroScheduler - 158885515 reads were filtered out during the traversal out of approximately 181931389 total reads (87.33%) 
    INFO  00:57:17,190 MicroScheduler -   -> 9210 reads (0.01% of total) failing BadCigarFilter 
    INFO  00:57:17,192 MicroScheduler -   -> 81066454 reads (44.56% of total) failing DuplicateReadFilter 
    INFO  00:57:17,193 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter 
    INFO  00:57:17,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
    INFO  00:57:17,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
    INFO  00:57:17,198 MicroScheduler -   -> 77809851 reads (42.77% of total) failing NotPrimaryAlignmentFilter 
    INFO  00:57:17,200 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
    ------------------------------------------------------------------------------------------
    Done. ------------------------------------------------------------------------------------------

**This is how STAR log summary looks:** 

                UNIQUE READS:
                   Uniquely mapped reads number |       29463720
                        Uniquely mapped reads % |       72.35%
                          Average mapped length |       271.00
                       Number of splices: Total |       21158459
            Number of splices: Annotated (sjdb) |       21067563
                       Number of splices: GT/AG |       20952149
                       Number of splices: GC/AG |       126813
                       Number of splices: AT/AC |       5622
               Number of splices: Non-canonical |       73875
                      Mismatch rate per base, % |       0.48%
                         Deletion rate per base |       0.02%
                        Deletion average length |       1.27
                        Insertion rate per base |       0.01%
                       Insertion average length |       1.84
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |       9507878
             % of reads mapped to multiple loci |       23.35%
        Number of reads mapped to too many loci |       355263
             % of reads mapped to too many loci |       0.87%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |       0.00%
                 % of reads unmapped: too short |       2.76%
                     % of reads unmapped: other |       0.67%
                                  CHIMERIC READS:
                       Number of chimeric reads |       0
                            % of chimeric reads |       0.00%




If you are sure you want to retain non primary and duplicates, I think you can add to mutect the option `--disable_read_filter NotPrimaryAlignmentFilter --disable_read_filter DuplicateReadFilter` (not tested). See some docs [here.][1]


  [1]: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php