## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg.bam --OUTPUT /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-sort-rg-dedup.bam --METRICS_FILE /project/scv/examples/bioinformatics/gatk/out/gatk_SRR062634_200_6400063/SRR062634-dedup-metric.txt --ASSUME_SORT_ORDER coordinate --CREATE_INDEX true --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri May 07 13:00:59 EDT 2021 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE SRR062634 3 195 19 7 0 1 0 0.005089 18947 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 193 193 2.0 1.989761 1 1 3.0 2.969387 0 0 4.0 3.938983 0 0 5.0 4.898652 0 0 6.0 5.848494 0 0 7.0 6.78861 0 0 8.0 7.719101 0 0 9.0 8.640064 0 0 10.0 9.551598 0 0 11.0 10.453798 0 0 12.0 11.346761 0 0 13.0 12.23058 0 0 14.0 13.10535 0 0 15.0 13.971163 0 0 16.0 14.828111 0 0 17.0 15.676285 0 0 18.0 16.515774 0 0 19.0 17.346667 0 0 20.0 18.169053 0 0 21.0 18.983018 0 0 22.0 19.788649 0 0 23.0 20.586032 0 0 24.0 21.375249 0 0 25.0 22.156386 0 0 26.0 22.929525 0 0 27.0 23.694747 0 0 28.0 24.452135 0 0 29.0 25.201767 0 0 30.0 25.943724 0 0 31.0 26.678084 0 0 32.0 27.404924 0 0 33.0 28.124323 0 0 34.0 28.836355 0 0 35.0 29.541097 0 0 36.0 30.238623 0 0 37.0 30.929007 0 0 38.0 31.612322 0 0 39.0 32.288641 0 0 40.0 32.958035 0 0 41.0 33.620574 0 0 42.0 34.27633 0 0 43.0 34.925372 0 0 44.0 35.567768 0 0 45.0 36.203586 0 0 46.0 36.832894 0 0 47.0 37.455759 0 0 48.0 38.072246 0 0 49.0 38.682421 0 0 50.0 39.286348 0 0 51.0 39.884092 0 0 52.0 40.475715 0 0 53.0 41.061281 0 0 54.0 41.64085 0 0 55.0 42.214486 0 0 56.0 42.782248 0 0 57.0 43.344197 0 0 58.0 43.900392 0 0 59.0 44.450892 0 0 60.0 44.995755 0 0 61.0 45.535039 0 0 62.0 46.068802 0 0 63.0 46.5971 0 0 64.0 47.119988 0 0 65.0 47.637522 0 0 66.0 48.149757 0 0 67.0 48.656747 0 0 68.0 49.158547 0 0 69.0 49.655208 0 0 70.0 50.146784 0 0 71.0 50.633326 0 0 72.0 51.114887 0 0 73.0 51.591517 0 0 74.0 52.063267 0 0 75.0 52.530187 0 0 76.0 52.992326 0 0 77.0 53.449732 0 0 78.0 53.902456 0 0 79.0 54.350544 0 0 80.0 54.794044 0 0 81.0 55.233003 0 0 82.0 55.667467 0 0 83.0 56.097483 0 0 84.0 56.523096 0 0 85.0 56.944351 0 0 86.0 57.361292 0 0 87.0 57.773965 0 0 88.0 58.182412 0 0 89.0 58.586677 0 0 90.0 58.986803 0 0 91.0 59.382832 0 0 92.0 59.774806 0 0 93.0 60.162767 0 0 94.0 60.546755 0 0 95.0 60.926811 0 0 96.0 61.302976 0 0 97.0 61.675289 0 0 98.0 62.043791 0 0 99.0 62.408519 0 0 100.0 62.769512 0 0