## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-08-18/FR_Ess_Vil_1_2014-08-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-08-18/FR_Ess_Vil_1_2014-08-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-08-18/FR_Ess_Vil_1_2014-08-18.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT 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 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 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 09:31:00 UTC 2023 ## 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 lib1 2385986 31177821 0 0 772786 1120558 0 0.046553 423281627 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 28380422 28380422 2.0 1.92899 869873 869873 3.0 2.792012 24394 24394 4.0 3.593751 1400 1400 5.0 4.338559 516 516 6.0 5.030477 364 364 7.0 5.673263 263 263 8.0 6.270404 191 191 9.0 6.825142 192 192 10.0 7.340488 159 159 11.0 7.819239 128 128 12.0 8.263995 113 113 13.0 8.677168 99 99 14.0 9.061001 88 88 15.0 9.417579 76 76 16.0 9.748836 70 70 17.0 10.05657 52 52 18.0 10.342452 81 81 19.0 10.608034 61 61 20.0 10.854757 43 43 21.0 11.083959 63 63 22.0 11.296886 47 47 23.0 11.494694 28 28 24.0 11.678455 43 43 25.0 11.849167 38 38 26.0 12.007756 40 40 27.0 12.155084 29 29 28.0 12.291951 25 25 29.0 12.419098 28 28 30.0 12.537217 27 27 31.0 12.646948 32 32 32.0 12.748888 38 38 33.0 12.843588 31 31 34.0 12.931564 29 29 35.0 13.013292 32 32 36.0 13.089217 28 28 37.0 13.159751 19 19 38.0 13.225276 22 22 39.0 13.286148 20 20 40.0 13.342698 22 22 41.0 13.395232 21 21 42.0 13.444035 17 17 43.0 13.489373 17 17 44.0 13.531492 25 25 45.0 13.570619 16 16 46.0 13.606968 17 17 47.0 13.640737 17 17 48.0 13.672107 11 11 49.0 13.701249 16 16 50.0 13.728322 8 8 51.0 13.753473 9 9 52.0 13.776838 12 12 53.0 13.798544 12 12 54.0 13.818708 12 12 55.0 13.83744 9 9 56.0 13.854842 8 8 57.0 13.871009 10 10 58.0 13.886027 13 13 59.0 13.89998 15 15 60.0 13.912941 11 11 61.0 13.924982 11 11 62.0 13.936168 9 9 63.0 13.946559 13 13 64.0 13.956213 12 12 65.0 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