## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2012-10-10/US_Cal_Tuo_1_2012-10-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2012-10-10/US_Cal_Tuo_1_2012-10-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2012-10-10/US_Cal_Tuo_1_2012-10-10.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 18:09:51 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 1002495 36265336 0 0 442047 3431595 0 0.099346 179337940 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 28711545 28711545 2.0 1.816917 2620793 2620793 3.0 2.48427 224149 224149 4.0 3.029442 26913 26913 5.0 3.474803 7559 7559 6.0 3.838625 3922 3922 7.0 4.135838 2346 2346 8.0 4.378636 1526 1526 9.0 4.576982 984 984 10.0 4.739014 702 702 11.0 4.871381 558 558 12.0 4.979513 384 384 13.0 5.067849 297 297 14.0 5.140011 234 234 15.0 5.198962 163 163 16.0 5.24712 141 141 17.0 5.286461 116 116 18.0 5.3186 99 99 19.0 5.344854 81 81 20.0 5.366302 61 61 21.0 5.383823 58 58 22.0 5.398136 52 52 23.0 5.409829 36 36 24.0 5.419381 36 36 25.0 5.427184 29 29 26.0 5.433558 28 28 27.0 5.438766 29 29 28.0 5.44302 31 31 29.0 5.446495 18 18 30.0 5.449334 18 18 31.0 5.451653 24 24 32.0 5.453548 18 18 33.0 5.455095 16 16 34.0 5.45636 19 19 35.0 5.457393 20 20 36.0 5.458236 21 21 37.0 5.458926 14 14 38.0 5.459489 25 25 39.0 5.459949 11 11 40.0 5.460325 11 11 41.0 5.460632 12 12 42.0 5.460882 11 11 43.0 5.461087 13 13 44.0 5.461255 14 14 45.0 5.461391 7 7 46.0 5.461503 11 11 47.0 5.461594 9 9 48.0 5.461669 6 6 49.0 5.46173 13 13 50.0 5.461779 7 7 51.0 5.46182 7 7 52.0 5.461853 4 4 53.0 5.46188 7 7 54.0 5.461903 7 7 55.0 5.461921 11 11 56.0 5.461935 7 7 57.0 5.461948 8 8 58.0 5.461957 7 7 59.0 5.461965 10 10 60.0 5.461972 7 7 61.0 5.461977 5 5 62.0 5.461982 5 5 63.0 5.461985 3 3 64.0 5.461988 3 3 65.0 5.461991 5 5 66.0 5.461993 4 4 67.0 5.461994 10 10 68.0 5.461996 4 4 69.0 5.461997 4 4 70.0 5.461998 6 6 71.0 5.461998 2 2 72.0 5.461999 5 5 73.0 5.461999 7 7 74.0 5.462 3 3 75.0 5.462 3 3 76.0 5.462 6 6 77.0 5.462 5 5 78.0 5.462001 7 7 79.0 5.462001 5 5 80.0 5.462001 3 3 81.0 5.462001 3 3 82.0 5.462001 2 2 83.0 5.462001 0 0 84.0 5.462001 4 4 85.0 5.462001 4 4 86.0 5.462001 4 4 87.0 5.462001 4 4 88.0 5.462001 4 4 89.0 5.462001 0 0 90.0 5.462001 3 3 91.0 5.462001 4 4 92.0 5.462001 2 2 93.0 5.462001 1 1 94.0 5.462001 2 2 95.0 5.462001 0 0 96.0 5.462001 1 1 97.0 5.462001 2 2 98.0 5.462001 3 3 99.0 5.462001 3 3 100.0 5.462001 1 1 101.0 0 1 1 102.0 0 3 3 103.0 0 2 2 104.0 0 5 5 106.0 0 1 1 110.0 0 1 1 111.0 0 4 4 112.0 0 1 1 113.0 0 1 1 114.0 0 1 1 115.0 0 2 2 117.0 0 1 1 118.0 0 1 1 119.0 0 1 1 121.0 0 1 1 122.0 0 2 2 123.0 0 1 1 124.0 0 3 3 125.0 0 2 2 126.0 0 1 1 127.0 0 1 1 128.0 0 3 3 129.0 0 3 3 130.0 0 2 2 131.0 0 3 3 132.0 0 1 1 133.0 0 2 2 134.0 0 2 2 136.0 0 3 3 137.0 0 2 2 138.0 0 2 2 140.0 0 4 4 144.0 0 1 1 145.0 0 1 1 146.0 0 1 1 149.0 0 2 2 150.0 0 1 1 152.0 0 3 3 153.0 0 2 2 155.0 0 1 1 157.0 0 1 1 158.0 0 1 1 159.0 0 1 1 160.0 0 2 2 168.0 0 1 1 169.0 0 1 1 170.0 0 1 1 175.0 0 1 1 181.0 0 1 1 182.0 0 3 3 183.0 0 1 1 184.0 0 2 2 185.0 0 1 1 186.0 0 1 1 194.0 0 1 1 198.0 0 1 1 199.0 0 1 1 200.0 0 2 2 201.0 0 1 1 203.0 0 1 1 206.0 0 1 1 211.0 0 1 1 214.0 0 1 1 215.0 0 1 1 216.0 0 3 3 217.0 0 1 1 222.0 0 1 1 224.0 0 1 1 227.0 0 1 1 228.0 0 1 1 236.0 0 1 1 241.0 0 1 1 245.0 0 1 1 249.0 0 2 2 250.0 0 1 1 254.0 0 2 2 255.0 0 1 1 267.0 0 1 1 268.0 0 1 1 269.0 0 1 1 273.0 0 2 2 276.0 0 1 1 285.0 0 1 1 308.0 0 1 1 311.0 0 1 1 323.0 0 1 1 326.0 0 1 1 344.0 0 1 1 352.0 0 1 1 365.0 0 1 1 368.0 0 1 1 372.0 0 1 1 382.0 0 1 1 393.0 0 1 1 397.0 0 1 1 435.0 0 1 1 442.0 0 1 1 456.0 0 1 1 476.0 0 1 1 494.0 0 1 1 507.0 0 1 1 510.0 0 1 1 520.0 0 1 1 524.0 0 1 1 543.0 0 1 1 546.0 0 1 1 565.0 0 1 1 574.0 0 1 1 580.0 0 1 1 589.0 0 1 1 591.0 0 1 1 594.0 0 1 1 608.0 0 1 1 612.0 0 1 1 614.0 0 1 1 634.0 0 1 1 637.0 0 1 1 645.0 0 1 1 665.0 0 1 1 690.0 0 1 1 726.0 0 1 1 769.0 0 1 1 772.0 0 1 1 776.0 0 1 1 791.0 0 1 1 886.0 0 1 1 910.0 0 1 1 915.0 0 1 1 919.0 0 1 1 926.0 0 1 1 942.0 0 1 1 969.0 0 1 1 992.0 0 1 1 1029.0 0 1 1 1117.0 0 1 1 1178.0 0 1 1 1207.0 0 1 1 1229.0 0 1 1 1245.0 0 1 1 1257.0 0 1 1 1263.0 0 1 1 1317.0 0 1 1 1398.0 0 1 1 1455.0 0 1 1 1502.0 0 1 1 1511.0 0 1 1 1624.0 0 1 1 1636.0 0 1 1 1643.0 0 1 1 1729.0 0 1 1 1789.0 0 1 1 1900.0 0 1 1 2047.0 0 1 1 2075.0 0 1 1 2202.0 0 1 1 2240.0 0 1 1 2537.0 0 1 1 2650.0 0 1 1 2825.0 0 1 1 2848.0 0 1 1 2988.0 0 1 1 3210.0 0 1 1 3387.0 0 1 1 4203.0 0 1 1 4431.0 0 1 1 4812.0 0 1 1 5444.0 0 1 1 7529.0 0 1 1