## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-08-31/US_Cal_Tuo_1_2013-08-31.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-08-31/US_Cal_Tuo_1_2013-08-31.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-08-31/US_Cal_Tuo_1_2013-08-31.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 18:24:22 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 6543942 48545944 0 0 2625564 1221245 0 0.048903 948628806 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 45568014 45568014 2.0 1.950113 810638 810638 3.0 2.852826 27365 27365 4.0 3.710506 5655 5655 5.0 4.525398 2532 2532 6.0 5.299638 1409 1409 7.0 6.035252 861 861 8.0 6.734168 580 580 9.0 7.398218 496 496 10.0 8.029139 344 344 11.0 8.628586 276 276 12.0 9.198127 238 238 13.0 9.739256 186 186 14.0 10.253389 193 193 15.0 10.741873 143 143 16.0 11.205988 122 122 17.0 11.64695 105 105 18.0 12.065913 90 90 19.0 12.463975 92 92 20.0 12.842179 66 66 21.0 13.201515 59 59 22.0 13.542925 81 81 23.0 13.867302 75 75 24.0 14.175497 55 55 25.0 14.468318 48 48 26.0 14.74653 53 53 27.0 15.010863 54 54 28.0 15.262008 56 56 29.0 15.500625 44 44 30.0 15.727338 38 38 31.0 15.942741 61 61 32.0 16.147398 45 45 33.0 16.341845 37 37 34.0 16.526591 28 28 35.0 16.702121 41 41 36.0 16.868895 39 39 37.0 17.027348 32 32 38.0 17.177897 39 39 39.0 17.320935 26 26 40.0 17.456837 30 30 41.0 17.585959 25 25 42.0 17.70864 26 26 43.0 17.825201 23 23 44.0 17.935947 16 16 45.0 18.041167 23 23 46.0 18.141139 19 19 47.0 18.236123 21 21 48.0 18.326369 26 26 49.0 18.412113 27 27 50.0 18.493579 20 20 51.0 18.570981 21 21 52.0 18.644521 22 22 53.0 18.714393 23 23 54.0 18.780779 20 20 55.0 18.843854 18 18 56.0 18.903781 10 10 57.0 18.960719 21 21 58.0 19.014817 15 15 59.0 19.066216 11 11 60.0 19.11505 16 16 61.0 19.161449 16 16 62.0 19.205532 13 13 63.0 19.247417 9 9 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