## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-09-15/DK_Mid_Kar_1_2016-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-09-15/DK_Mid_Kar_1_2016-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-09-15/DK_Mid_Kar_1_2016-09-15.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 09:05:26 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 34329599 11489768 0 0 8507333 948112 0 0.181534 65734767 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 9578029 9578029 2.0 1.839633 633157 633157 3.0 2.544618 49813 49813 4.0 3.136546 5913 5913 5.0 3.633549 1916 1916 6.0 4.05085 1069 1069 7.0 4.401229 733 733 8.0 4.695419 544 544 9.0 4.942431 396 396 10.0 5.149831 336 336 11.0 5.32397 268 268 12.0 5.470184 254 254 13.0 5.592949 197 197 14.0 5.696027 175 175 15.0 5.782575 140 140 16.0 5.855244 139 139 17.0 5.916259 123 123 18.0 5.967489 109 109 19.0 6.010503 138 138 20.0 6.04662 115 115 21.0 6.076945 95 95 22.0 6.102406 107 107 23.0 6.123784 98 98 24.0 6.141734 83 83 25.0 6.156806 67 67 26.0 6.16946 70 70 27.0 6.180085 73 73 28.0 6.189007 58 58 29.0 6.196497 68 68 30.0 6.202786 48 48 31.0 6.208067 56 56 32.0 6.212501 55 55 33.0 6.216224 52 52 34.0 6.21935 45 45 35.0 6.221974 31 31 36.0 6.224178 33 33 37.0 6.226028 40 40 38.0 6.227582 24 24 39.0 6.228886 24 24 40.0 6.229981 34 34 41.0 6.230901 19 19 42.0 6.231673 32 32 43.0 6.232321 21 21 44.0 6.232865 35 35 45.0 6.233323 16 16 46.0 6.233706 17 17 47.0 6.234028 12 12 48.0 6.234299 14 14 49.0 6.234526 22 22 50.0 6.234717 19 19 51.0 6.234877 15 15 52.0 6.235011 21 21 53.0 6.235124 17 17 54.0 6.235219 21 21 55.0 6.235299 16 16 56.0 6.235366 11 11 57.0 6.235422 21 21 58.0 6.235469 10 10 59.0 6.235508 12 12 60.0 6.235542 13 13 61.0 6.235569 17 17 62.0 6.235593 17 17 63.0 6.235613 8 8 64.0 6.235629 9 9 65.0 6.235643 9 9 66.0 6.235655 8 8 67.0 6.235664 10 10 68.0 6.235672 14 14 69.0 6.235679 14 14 70.0 6.235685 16 16 71.0 6.23569 9 9 72.0 6.235694 16 16 73.0 6.235698 11 11 74.0 6.2357 7 7 75.0 6.235703 11 11 76.0 6.235705 10 10 77.0 6.235707 10 10 78.0 6.235708 5 5 79.0 6.235709 10 10 80.0 6.23571 14 14 81.0 6.235711 10 10 82.0 6.235712 8 8 83.0 6.235712 12 12 84.0 6.235713 9 9 85.0 6.235713 9 9 86.0 6.235714 6 6 87.0 6.235714 5 5 88.0 6.235714 6 6 89.0 6.235714 8 8 90.0 6.235715 7 7 91.0 6.235715 8 8 92.0 6.235715 5 5 93.0 6.235715 4 4 94.0 6.235715 11 11 95.0 6.235715 4 4 96.0 6.235715 8 8 97.0 6.235715 7 7 98.0 6.235715 4 4 99.0 6.235715 6 6 100.0 6.235715 5 5 101.0 0 9 9 102.0 0 5 5 103.0 0 5 5 104.0 0 7 7 105.0 0 5 5 106.0 0 5 5 107.0 0 1 1 108.0 0 5 5 109.0 0 6 6 110.0 0 5 5 112.0 0 3 3 113.0 0 6 6 114.0 0 10 10 115.0 0 3 3 116.0 0 3 3 117.0 0 3 3 118.0 0 1 1 119.0 0 4 4 120.0 0 4 4 121.0 0 1 1 122.0 0 5 5 123.0 0 4 4 124.0 0 2 2 125.0 0 1 1 126.0 0 6 6 127.0 0 3 3 129.0 0 4 4 130.0 0 4 4 131.0 0 2 2 132.0 0 1 1 133.0 0 1 1 134.0 0 3 3 135.0 0 5 5 136.0 0 1 1 137.0 0 1 1 138.0 0 2 2 139.0 0 1 1 140.0 0 3 3 141.0 0 2 2 142.0 0 2 2 143.0 0 3 3 144.0 0 1 1 146.0 0 1 1 147.0 0 1 1 148.0 0 5 5 150.0 0 3 3 152.0 0 1 1 153.0 0 2 2 154.0 0 3 3 155.0 0 1 1 156.0 0 1 1 157.0 0 1 1 158.0 0 1 1 159.0 0 3 3 160.0 0 3 3 161.0 0 3 3 163.0 0 2 2 164.0 0 1 1 165.0 0 3 3 166.0 0 1 1 167.0 0 3 3 169.0 0 2 2 171.0 0 2 2 172.0 0 1 1 173.0 0 1 1 174.0 0 1 1 176.0 0 2 2 177.0 0 2 2 179.0 0 2 2 180.0 0 1 1 181.0 0 2 2 182.0 0 1 1 183.0 0 1 1 185.0 0 2 2 186.0 0 1 1 189.0 0 1 1 190.0 0 2 2 192.0 0 1 1 196.0 0 1 1 197.0 0 1 1 199.0 0 5 5 201.0 0 1 1 204.0 0 1 1 205.0 0 1 1 206.0 0 3 3 207.0 0 1 1 208.0 0 1 1 209.0 0 1 1 210.0 0 1 1 212.0 0 1 1 213.0 0 3 3 214.0 0 1 1 215.0 0 1 1 216.0 0 1 1 217.0 0 1 1 220.0 0 1 1 221.0 0 1 1 223.0 0 3 3 228.0 0 2 2 230.0 0 1 1 231.0 0 1 1 233.0 0 1 1 236.0 0 1 1 247.0 0 1 1 249.0 0 1 1 250.0 0 1 1 252.0 0 1 1 255.0 0 2 2 256.0 0 1 1 262.0 0 1 1 263.0 0 2 2 272.0 0 1 1 275.0 0 1 1 286.0 0 1 1 292.0 0 1 1 296.0 0 1 1 297.0 0 1 1 300.0 0 1 1 301.0 0 2 2 305.0 0 1 1 314.0 0 1 1 317.0 0 1 1 321.0 0 1 1 322.0 0 1 1 323.0 0 2 2 324.0 0 1 1 326.0 0 1 1 355.0 0 1 1 368.0 0 1 1 369.0 0 1 1 386.0 0 1 1 387.0 0 1 1 389.0 0 1 1 390.0 0 1 1 393.0 0 1 1 402.0 0 1 1 404.0 0 1 1 405.0 0 1 1 407.0 0 1 1 414.0 0 1 1 418.0 0 1 1 419.0 0 1 1 434.0 0 1 1 444.0 0 1 1 454.0 0 1 1 461.0 0 1 1 509.0 0 1 1 545.0 0 1 1 610.0 0 1 1 633.0 0 1 1 705.0 0 1 1 710.0 0 1 1 750.0 0 1 1 783.0 0 1 1 856.0 0 1 1 1068.0 0 1 1 1186.0 0 1 1 1197.0 0 1 1 1235.0 0 1 1 1443.0 0 1 1 1445.0 0 1 1 1831.0 0 1 1 3505.0 0 1 1