## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-11-18/US_Cal_Pla_1_2012-11-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-11-18/US_Cal_Pla_1_2012-11-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2012-11-18/US_Cal_Pla_1_2012-11-18.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 17:18:20 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 845702 27099739 0 0 232024 1514185 0 0.059231 233385354 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 24284935 24284935 2.0 1.890372 817169 817169 3.0 2.683134 27197 27197 4.0 3.388988 2926 2926 5.0 4.01746 1380 1380 6.0 4.577034 942 942 7.0 5.075264 651 651 8.0 5.518873 499 499 9.0 5.91385 366 366 10.0 6.265527 316 316 11.0 6.57865 264 264 12.0 6.857446 192 192 13.0 7.105679 172 172 14.0 7.326698 164 164 15.0 7.523487 122 122 16.0 7.698703 147 147 17.0 7.85471 102 102 18.0 7.993614 75 75 19.0 8.117291 83 83 20.0 8.227409 97 97 21.0 8.325455 85 85 22.0 8.412753 70 70 23.0 8.49048 80 80 24.0 8.559686 71 71 25.0 8.621306 73 73 26.0 8.67617 57 57 27.0 8.725019 39 39 28.0 8.768513 36 36 29.0 8.807239 60 60 30.0 8.84172 50 50 31.0 8.87242 38 38 32.0 8.899755 42 42 33.0 8.924094 44 44 34.0 8.945764 41 41 35.0 8.965058 52 52 36.0 8.982237 43 43 37.0 8.997533 37 37 38.0 9.011152 29 29 39.0 9.023278 33 33 40.0 9.034075 25 25 41.0 9.043688 22 22 42.0 9.052247 27 27 43.0 9.059868 19 19 44.0 9.066653 31 31 45.0 9.072695 17 17 46.0 9.078074 19 19 47.0 9.082864 24 24 48.0 9.087128 31 31 49.0 9.090925 20 20 50.0 9.094306 18 18 51.0 9.097316 19 19 52.0 9.099996 13 13 53.0 9.102382 14 14 54.0 9.104507 20 20 55.0 9.106398 12 12 56.0 9.108083 16 16 57.0 9.109583 16 16 58.0 9.110918 19 19 59.0 9.112107 21 21 60.0 9.113165 10 10 61.0 9.114108 14 14 62.0 9.114947 13 13 63.0 9.115694 10 10 64.0 9.11636 11 11 65.0 9.116952 9 9 66.0 9.117479 13 13 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