## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/home/siebrenf/tdewijs/results/star/GRCg6a-GSM1481263.samtools-coordinate-unsieved.bam] OUTPUT=/home/siebrenf/tdewijs/results/star/GRCg6a-GSM1481263.samtools-coordinate-dupmarked.bam METRICS_FILE=/home/siebrenf/tdewijs/results/qc/markdup/GRCg6a-GSM1481263.samtools-coordinate.metrics.txt MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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_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: Thu Dec 09 20:28:19 CET 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 Unknown Library 0 22375524 1484300 0 0 4088767 0 0.182734 53513412 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16673562 16673562 2.0 1.658277 1004320 1004320 3.0 2.091606 261974 261974 4.0 2.376856 115510 115510 5.0 2.56463 62995 62995 6.0 2.688237 39611 39611 7.0 2.769605 26353 26353 8.0 2.823168 18918 18918 9.0 2.858427 13697 13697 10.0 2.881637 10558 10558 11.0 2.896916 8405 8405 12.0 2.906973 6699 6699 13.0 2.913594 5377 5377 14.0 2.917952 4435 4435 15.0 2.920821 3685 3685 16.0 2.92271 3073 3073 17.0 2.923953 2672 2672 18.0 2.924771 2238 2238 19.0 2.92531 2008 2008 20.0 2.925665 1807 1807 21.0 2.925898 1564 1564 22.0 2.926052 1328 1328 23.0 2.926153 1199 1199 24.0 2.92622 1110 1110 25.0 2.926263 970 970 26.0 2.926292 894 894 27.0 2.926311 746 746 28.0 2.926324 698 698 29.0 2.926332 597 597 30.0 2.926337 590 590 31.0 2.926341 530 530 32.0 2.926343 510 510 33.0 2.926345 466 466 34.0 2.926346 415 415 35.0 2.926347 363 363 36.0 2.926347 324 324 37.0 2.926347 347 347 38.0 2.926347 302 302 39.0 2.926348 284 284 40.0 2.926348 287 287 41.0 2.926348 273 273 42.0 2.926348 226 226 43.0 2.926348 215 215 44.0 2.926348 214 214 45.0 2.926348 197 197 46.0 2.926348 175 175 47.0 2.926348 172 172 48.0 2.926348 171 171 49.0 2.926348 165 165 50.0 2.926348 150 150 51.0 2.926348 128 128 52.0 2.926348 122 122 53.0 2.926348 131 131 54.0 2.926348 114 114 55.0 2.926348 120 120 56.0 2.926348 106 106 57.0 2.926348 87 87 58.0 2.926348 85 85 59.0 2.926348 89 89 60.0 2.926348 81 81 61.0 2.926348 81 81 62.0 2.926348 99 99 63.0 2.926348 76 76 64.0 2.926348 60 60 65.0 2.926348 76 76 66.0 2.926348 58 58 67.0 2.926348 55 55 68.0 2.926348 48 48 69.0 2.926348 49 49 70.0 2.926348 59 59 71.0 2.926348 50 50 72.0 2.926348 54 54 73.0 2.926348 50 50 74.0 2.926348 46 46 75.0 2.926348 42 42 76.0 2.926348 41 41 77.0 2.926348 35 35 78.0 2.926348 42 42 79.0 2.926348 38 38 80.0 2.926348 36 36 81.0 2.926348 30 30 82.0 2.926348 26 26 83.0 2.926348 27 27 84.0 2.926348 41 41 85.0 2.926348 25 25 86.0 2.926348 23 23 87.0 2.926348 23 23 88.0 2.926348 29 29 89.0 2.926348 20 20 90.0 2.926348 30 30 91.0 2.926348 23 23 92.0 2.926348 26 26 93.0 2.926348 17 17 94.0 2.926348 20 20 95.0 2.926348 24 24 96.0 2.926348 18 18 97.0 2.926348 29 29 98.0 2.926348 22 22 99.0 2.926348 25 25 100.0 2.926348 19 19 101.0 0 22 22 102.0 0 13 13 103.0 0 14 14 104.0 0 14 14 105.0 0 12 12 106.0 0 12 12 107.0 0 12 12 108.0 0 14 14 109.0 0 13 13 110.0 0 16 16 111.0 0 11 11 112.0 0 13 13 113.0 0 13 13 114.0 0 18 18 115.0 0 9 9 116.0 0 8 8 117.0 0 12 12 118.0 0 8 8 119.0 0 4 4 120.0 0 8 8 121.0 0 6 6 122.0 0 11 11 123.0 0 12 12 124.0 0 7 7 125.0 0 10 10 126.0 0 8 8 127.0 0 5 5 128.0 0 8 8 129.0 0 6 6 130.0 0 9 9 131.0 0 7 7 132.0 0 2 2 133.0 0 7 7 134.0 0 9 9 135.0 0 3 3 136.0 0 10 10 137.0 0 9 9 138.0 0 4 4 139.0 0 10 10 140.0 0 7 7 141.0 0 9 9 142.0 0 6 6 143.0 0 6 6 144.0 0 5 5 145.0 0 1 1 146.0 0 2 2 147.0 0 4 4 148.0 0 3 3 149.0 0 6 6 150.0 0 7 7 151.0 0 4 4 152.0 0 3 3 153.0 0 5 5 154.0 0 2 2 155.0 0 6 6 156.0 0 7 7 157.0 0 1 1 158.0 0 3 3 159.0 0 2 2 160.0 0 4 4 161.0 0 6 6 162.0 0 2 2 163.0 0 3 3 164.0 0 2 2 165.0 0 2 2 167.0 0 7 7 168.0 0 2 2 169.0 0 1 1 170.0 0 1 1 171.0 0 4 4 172.0 0 5 5 173.0 0 6 6 174.0 0 1 1 175.0 0 5 5 176.0 0 2 2 177.0 0 2 2 178.0 0 5 5 179.0 0 4 4 180.0 0 5 5 181.0 0 4 4 182.0 0 4 4 183.0 0 1 1 184.0 0 3 3 185.0 0 2 2 186.0 0 1 1 187.0 0 1 1 188.0 0 2 2 189.0 0 1 1 190.0 0 8 8 191.0 0 2 2 192.0 0 1 1 194.0 0 3 3 195.0 0 2 2 196.0 0 2 2 197.0 0 2 2 198.0 0 1 1 200.0 0 1 1 201.0 0 3 3 202.0 0 2 2 203.0 0 2 2 204.0 0 1 1 205.0 0 3 3 206.0 0 2 2 208.0 0 2 2 209.0 0 1 1 212.0 0 1 1 213.0 0 2 2 214.0 0 2 2 216.0 0 2 2 218.0 0 2 2 219.0 0 1 1 220.0 0 3 3 221.0 0 1 1 222.0 0 1 1 223.0 0 2 2 228.0 0 2 2 229.0 0 1 1 230.0 0 1 1 232.0 0 1 1 233.0 0 1 1 234.0 0 1 1 235.0 0 2 2 239.0 0 1 1 244.0 0 4 4 246.0 0 1 1 250.0 0 5 5 251.0 0 1 1 253.0 0 2 2 254.0 0 1 1 255.0 0 1 1 259.0 0 1 1 261.0 0 1 1 262.0 0 1 1 263.0 0 2 2 266.0 0 1 1 269.0 0 1 1 271.0 0 1 1 272.0 0 1 1 274.0 0 1 1 277.0 0 3 3 278.0 0 1 1 279.0 0 1 1 284.0 0 4 4 285.0 0 1 1 289.0 0 1 1 292.0 0 2 2 294.0 0 3 3 297.0 0 1 1 299.0 0 1 1 300.0 0 1 1 302.0 0 1 1 303.0 0 1 1 306.0 0 2 2 308.0 0 1 1 312.0 0 1 1 313.0 0 1 1 315.0 0 1 1 324.0 0 2 2 329.0 0 1 1 334.0 0 2 2 335.0 0 1 1 339.0 0 1 1 349.0 0 1 1 350.0 0 2 2 352.0 0 1 1 361.0 0 1 1 362.0 0 1 1 364.0 0 1 1 370.0 0 1 1 379.0 0 1 1 380.0 0 1 1 395.0 0 1 1 397.0 0 1 1 409.0 0 1 1 416.0 0 1 1 418.0 0 1 1 421.0 0 1 1 424.0 0 1 1 427.0 0 1 1 431.0 0 1 1 433.0 0 1 1 444.0 0 1 1 459.0 0 1 1 463.0 0 1 1 464.0 0 1 1 499.0 0 1 1 504.0 0 1 1 581.0 0 1 1 614.0 0 1 1 648.0 0 1 1 663.0 0 1 1 790.0 0 1 1 863.0 0 1 1 1106.0 0 1 1