## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-08-23/RU_Nov_Val_1_2016-08-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-08-23/RU_Nov_Val_1_2016-08-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-08-23/RU_Nov_Val_1_2016-08-23.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 09:11:06 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 28260853 15601060 0 0 7032245 1189544 0 0.158272 97035928 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 13160026 13160026 2.0 1.851483 853815 853815 3.0 2.576505 61482 61482 4.0 3.19385 6578 6578 5.0 3.719508 2028 2028 6.0 4.167096 1185 1185 7.0 4.54821 800 800 8.0 4.872722 602 602 9.0 5.149039 458 458 10.0 5.384317 336 336 11.0 5.584653 284 284 12.0 5.755235 289 289 13.0 5.900483 238 238 14.0 6.024159 197 197 15.0 6.129467 181 181 16.0 6.219135 182 182 17.0 6.295486 136 136 18.0 6.360497 158 158 19.0 6.415853 129 129 20.0 6.462988 113 113 21.0 6.503122 108 108 22.0 6.537296 108 108 23.0 6.566394 97 97 24.0 6.591171 103 103 25.0 6.612268 91 91 26.0 6.630232 76 76 27.0 6.645527 85 85 28.0 6.658551 69 69 29.0 6.669641 71 71 30.0 6.679084 50 50 31.0 6.687124 57 57 32.0 6.693971 60 60 33.0 6.6998 42 42 34.0 6.704764 46 46 35.0 6.70899 29 29 36.0 6.712589 41 41 37.0 6.715653 44 44 38.0 6.718262 34 34 39.0 6.720484 36 36 40.0 6.722376 36 36 41.0 6.723987 34 34 42.0 6.725358 24 24 43.0 6.726526 34 34 44.0 6.72752 23 23 45.0 6.728367 34 34 46.0 6.729088 24 24 47.0 6.729702 24 24 48.0 6.730225 13 13 49.0 6.73067 14 14 50.0 6.731049 12 12 51.0 6.731371 18 18 52.0 6.731646 16 16 53.0 6.73188 14 14 54.0 6.732079 15 15 55.0 6.732249 19 19 56.0 6.732393 14 14 57.0 6.732516 10 10 58.0 6.732621 16 16 59.0 6.73271 12 12 60.0 6.732786 18 18 61.0 6.732851 15 15 62.0 6.732906 14 14 63.0 6.732953 12 12 64.0 6.732993 14 14 65.0 6.733027 13 13 66.0 6.733056 14 14 67.0 6.73308 8 8 68.0 6.733101 16 16 69.0 6.733119 12 12 70.0 6.733134 8 8 71.0 6.733147 10 10 72.0 6.733158 11 11 73.0 6.733168 11 11 74.0 6.733176 15 15 75.0 6.733182 19 19 76.0 6.733188 14 14 77.0 6.733193 13 13 78.0 6.733197 8 8 79.0 6.733201 13 13 80.0 6.733204 12 12 81.0 6.733207 10 10 82.0 6.733209 13 13 83.0 6.733211 11 11 84.0 6.733212 10 10 85.0 6.733214 7 7 86.0 6.733215 8 8 87.0 6.733216 9 9 88.0 6.733217 10 10 89.0 6.733217 3 3 90.0 6.733218 14 14 91.0 6.733218 7 7 92.0 6.733219 14 14 93.0 6.733219 13 13 94.0 6.73322 7 7 95.0 6.73322 9 9 96.0 6.73322 5 5 97.0 6.73322 6 6 98.0 6.73322 3 3 99.0 6.733221 8 8 100.0 6.733221 7 7 101.0 0 4 4 102.0 0 5 5 103.0 0 6 6 104.0 0 4 4 105.0 0 8 8 106.0 0 4 4 107.0 0 3 3 108.0 0 6 6 109.0 0 6 6 110.0 0 7 7 111.0 0 5 5 112.0 0 2 2 113.0 0 4 4 114.0 0 6 6 115.0 0 2 2 116.0 0 5 5 117.0 0 4 4 118.0 0 1 1 119.0 0 5 5 120.0 0 3 3 121.0 0 1 1 122.0 0 4 4 123.0 0 5 5 124.0 0 4 4 125.0 0 1 1 126.0 0 4 4 127.0 0 3 3 128.0 0 3 3 129.0 0 3 3 130.0 0 3 3 131.0 0 2 2 132.0 0 3 3 133.0 0 2 2 134.0 0 2 2 135.0 0 1 1 136.0 0 3 3 138.0 0 1 1 139.0 0 3 3 140.0 0 1 1 141.0 0 2 2 142.0 0 3 3 143.0 0 2 2 144.0 0 3 3 145.0 0 2 2 147.0 0 1 1 148.0 0 2 2 152.0 0 2 2 153.0 0 4 4 154.0 0 2 2 155.0 0 2 2 156.0 0 3 3 158.0 0 1 1 159.0 0 2 2 160.0 0 2 2 161.0 0 2 2 162.0 0 1 1 165.0 0 2 2 168.0 0 2 2 169.0 0 1 1 171.0 0 3 3 172.0 0 3 3 174.0 0 1 1 175.0 0 2 2 176.0 0 1 1 177.0 0 3 3 178.0 0 2 2 180.0 0 1 1 181.0 0 4 4 186.0 0 2 2 187.0 0 1 1 189.0 0 1 1 192.0 0 2 2 193.0 0 1 1 194.0 0 1 1 195.0 0 3 3 197.0 0 1 1 198.0 0 2 2 201.0 0 2 2 202.0 0 1 1 205.0 0 1 1 206.0 0 2 2 209.0 0 1 1 210.0 0 1 1 213.0 0 1 1 215.0 0 1 1 217.0 0 2 2 219.0 0 2 2 226.0 0 1 1 227.0 0 1 1 229.0 0 1 1 230.0 0 1 1 231.0 0 1 1 232.0 0 1 1 235.0 0 1 1 236.0 0 2 2 237.0 0 1 1 248.0 0 1 1 249.0 0 2 2 250.0 0 1 1 257.0 0 1 1 260.0 0 2 2 261.0 0 2 2 267.0 0 1 1 275.0 0 1 1 279.0 0 2 2 281.0 0 1 1 282.0 0 2 2 287.0 0 2 2 288.0 0 1 1 290.0 0 1 1 292.0 0 1 1 293.0 0 1 1 296.0 0 1 1 314.0 0 1 1 316.0 0 1 1 319.0 0 1 1 325.0 0 1 1 337.0 0 1 1 341.0 0 1 1 343.0 0 1 1 357.0 0 1 1 358.0 0 2 2 365.0 0 1 1 370.0 0 1 1 373.0 0 1 1 384.0 0 1 1 391.0 0 1 1 395.0 0 1 1 410.0 0 1 1 426.0 0 1 1 430.0 0 1 1 436.0 0 1 1 598.0 0 1 1 634.0 0 1 1 657.0 0 1 1 741.0 0 1 1 879.0 0 1 1