## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2014-08-17/RU_Nov_Val_1_2014-08-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2014-08-17/RU_Nov_Val_1_2014-08-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2014-08-17/RU_Nov_Val_1_2014-08-17.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 10:36:41 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 6938373 38379291 0 0 2549011 1092694 0 0.056566 661153707 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 35566025 35566025 2.0 1.943604 755439 755439 3.0 2.833992 16985 16985 4.0 3.674165 1902 1902 5.0 4.466956 875 875 6.0 5.215036 582 582 7.0 5.920928 430 430 8.0 6.58701 299 299 9.0 7.215527 255 255 10.0 7.808598 188 188 11.0 8.368222 174 174 12.0 8.896286 154 154 13.0 9.394569 112 112 14.0 9.86475 110 110 15.0 10.308415 101 101 16.0 10.727059 87 87 17.0 11.122093 89 89 18.0 11.494849 72 72 19.0 11.846582 59 59 20.0 12.178479 65 65 21.0 12.491658 66 66 22.0 12.787176 52 52 23.0 13.066027 48 48 24.0 13.329152 59 59 25.0 13.577437 43 43 26.0 13.811721 39 39 27.0 14.032791 47 47 28.0 14.241394 35 35 29.0 14.438233 43 43 30.0 14.623971 39 39 31.0 14.799233 30 30 32.0 14.964612 32 32 33.0 15.120664 35 35 34.0 15.267915 27 27 35.0 15.406862 19 19 36.0 15.537972 20 20 37.0 15.661689 30 30 38.0 15.778428 29 29 39.0 15.888584 26 26 40.0 15.992527 17 17 41.0 16.090608 13 13 42.0 16.183158 24 24 43.0 16.270488 21 21 44.0 16.352894 19 19 45.0 16.430652 14 14 46.0 16.504024 14 14 47.0 16.573259 22 22 48.0 16.638589 18 18 49.0 16.700235 11 11 50.0 16.758404 20 20 51.0 16.813293 23 23 52.0 16.865086 14 14 53.0 16.913958 17 17 54.0 16.960074 16 16 55.0 17.003589 12 12 56.0 17.044651 16 16 57.0 17.083396 8 8 58.0 17.119956 12 12 59.0 17.154455 13 13 60.0 17.187008 14 14 61.0 17.217725 14 14 62.0 17.246709 15 15 63.0 17.27406 8 8 64.0 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