## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-06-25/TR_Ank_Yes_1_2016-06-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-06-25/TR_Ank_Yes_1_2016-06-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-06-25/TR_Ank_Yes_1_2016-06-25.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 08:37:52 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 29941277 8008931 0 0 6615545 680021 0 0.173536 44453259 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 6644248 6644248 2.0 1.835132 404073 404073 3.0 2.532578 31445 31445 4.0 3.115038 4391 4391 5.0 3.601468 1640 1640 6.0 4.007702 982 982 7.0 4.346961 630 630 8.0 4.630287 491 491 9.0 4.866902 390 390 10.0 5.064507 287 287 11.0 5.229533 222 222 12.0 5.367351 188 188 13.0 5.482448 186 186 14.0 5.578569 156 156 15.0 5.658843 136 136 16.0 5.725882 150 150 17.0 5.781869 123 123 18.0 5.828625 116 116 19.0 5.867672 116 116 20.0 5.900282 106 106 21.0 5.927516 100 100 22.0 5.950259 88 88 23.0 5.969253 93 93 24.0 5.985116 80 80 25.0 5.998363 118 118 26.0 6.009426 81 81 27.0 6.018666 67 67 28.0 6.026382 63 63 29.0 6.032825 54 54 30.0 6.038207 57 57 31.0 6.042701 57 57 32.0 6.046454 54 54 33.0 6.049589 51 51 34.0 6.052207 44 44 35.0 6.054393 44 44 36.0 6.056219 45 45 37.0 6.057743 23 23 38.0 6.059017 34 34 39.0 6.06008 31 31 40.0 6.060968 26 26 41.0 6.06171 28 28 42.0 6.062329 29 29 43.0 6.062846 30 30 44.0 6.063278 24 24 45.0 6.063639 24 24 46.0 6.06394 16 16 47.0 6.064192 19 19 48.0 6.064402 18 18 49.0 6.064578 19 19 50.0 6.064724 16 16 51.0 6.064847 23 23 52.0 6.064949 8 8 53.0 6.065034 21 21 54.0 6.065106 17 17 55.0 6.065165 18 18 56.0 6.065215 14 14 57.0 6.065256 18 18 58.0 6.065291 13 13 59.0 6.06532 22 22 60.0 6.065344 10 10 61.0 6.065364 12 12 62.0 6.065381 15 15 63.0 6.065395 14 14 64.0 6.065407 9 9 65.0 6.065417 12 12 66.0 6.065425 15 15 67.0 6.065432 11 11 68.0 6.065438 12 12 69.0 6.065442 9 9 70.0 6.065446 12 12 71.0 6.06545 12 12 72.0 6.065453 16 16 73.0 6.065455 14 14 74.0 6.065457 3 3 75.0 6.065458 10 10 76.0 6.06546 14 14 77.0 6.065461 12 12 78.0 6.065462 11 11 79.0 6.065463 10 10 80.0 6.065463 6 6 81.0 6.065464 16 16 82.0 6.065464 13 13 83.0 6.065465 5 5 84.0 6.065465 11 11 85.0 6.065465 11 11 86.0 6.065465 11 11 87.0 6.065466 9 9 88.0 6.065466 8 8 89.0 6.065466 4 4 90.0 6.065466 12 12 91.0 6.065466 9 9 92.0 6.065466 7 7 93.0 6.065466 10 10 94.0 6.065466 9 9 95.0 6.065466 4 4 96.0 6.065466 8 8 97.0 6.065466 7 7 98.0 6.065466 9 9 99.0 6.065467 7 7 100.0 6.065467 10 10 101.0 0 3 3 102.0 0 9 9 103.0 0 4 4 104.0 0 5 5 105.0 0 8 8 106.0 0 3 3 107.0 0 2 2 108.0 0 4 4 109.0 0 3 3 110.0 0 7 7 111.0 0 4 4 112.0 0 4 4 113.0 0 3 3 114.0 0 3 3 115.0 0 4 4 116.0 0 4 4 117.0 0 3 3 118.0 0 4 4 119.0 0 4 4 120.0 0 5 5 121.0 0 5 5 122.0 0 7 7 124.0 0 5 5 125.0 0 3 3 126.0 0 6 6 127.0 0 5 5 128.0 0 1 1 129.0 0 5 5 130.0 0 4 4 131.0 0 3 3 132.0 0 4 4 133.0 0 2 2 134.0 0 3 3 135.0 0 1 1 136.0 0 2 2 137.0 0 2 2 138.0 0 2 2 139.0 0 1 1 140.0 0 1 1 141.0 0 1 1 142.0 0 1 1 143.0 0 2 2 144.0 0 5 5 145.0 0 4 4 146.0 0 2 2 147.0 0 2 2 148.0 0 1 1 149.0 0 5 5 150.0 0 1 1 153.0 0 3 3 154.0 0 2 2 155.0 0 3 3 156.0 0 3 3 157.0 0 1 1 158.0 0 1 1 159.0 0 2 2 160.0 0 3 3 161.0 0 1 1 162.0 0 1 1 163.0 0 1 1 164.0 0 3 3 165.0 0 2 2 166.0 0 2 2 167.0 0 3 3 168.0 0 1 1 169.0 0 3 3 171.0 0 1 1 174.0 0 1 1 175.0 0 2 2 176.0 0 1 1 177.0 0 1 1 179.0 0 3 3 180.0 0 1 1 181.0 0 3 3 182.0 0 4 4 183.0 0 1 1 184.0 0 1 1 186.0 0 1 1 189.0 0 2 2 193.0 0 1 1 194.0 0 1 1 197.0 0 1 1 199.0 0 1 1 202.0 0 1 1 205.0 0 1 1 206.0 0 1 1 208.0 0 1 1 209.0 0 1 1 211.0 0 1 1 212.0 0 1 1 213.0 0 1 1 214.0 0 1 1 215.0 0 1 1 218.0 0 1 1 219.0 0 1 1 221.0 0 1 1 223.0 0 2 2 226.0 0 1 1 228.0 0 1 1 229.0 0 1 1 230.0 0 3 3 231.0 0 1 1 232.0 0 1 1 234.0 0 1 1 235.0 0 1 1 236.0 0 1 1 238.0 0 1 1 242.0 0 1 1 244.0 0 1 1 245.0 0 2 2 247.0 0 1 1 248.0 0 1 1 249.0 0 2 2 250.0 0 1 1 251.0 0 1 1 253.0 0 1 1 254.0 0 1 1 255.0 0 1 1 256.0 0 1 1 257.0 0 1 1 258.0 0 1 1 261.0 0 2 2 263.0 0 1 1 266.0 0 2 2 271.0 0 2 2 276.0 0 1 1 277.0 0 1 1 281.0 0 1 1 282.0 0 2 2 283.0 0 1 1 290.0 0 2 2 294.0 0 1 1 307.0 0 2 2 308.0 0 1 1 313.0 0 1 1 315.0 0 1 1 320.0 0 1 1 323.0 0 1 1 327.0 0 1 1 328.0 0 1 1 333.0 0 2 2 335.0 0 1 1 347.0 0 1 1 349.0 0 1 1 350.0 0 1 1 352.0 0 2 2 357.0 0 1 1 361.0 0 1 1 364.0 0 1 1 365.0 0 1 1 368.0 0 1 1 369.0 0 1 1 375.0 0 1 1 377.0 0 1 1 379.0 0 1 1 386.0 0 1 1 403.0 0 1 1 412.0 0 1 1 429.0 0 1 1 457.0 0 1 1 468.0 0 1 1 484.0 0 1 1 518.0 0 2 2 526.0 0 1 1 529.0 0 1 1 540.0 0 1 1 548.0 0 1 1 582.0 0 1 1 652.0 0 1 1 766.0 0 2 2 769.0 0 1 1 782.0 0 1 1 949.0 0 1 1 1084.0 0 1 1 1538.0 0 1 1 2915.0 0 1 1