## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-03/UA_Ode_Ode_1_2014-07-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-03/UA_Ode_Ode_1_2014-07-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-03/UA_Ode_Ode_1_2014-07-03.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 16:59:30 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 4746408 23315286 0 0 1100004 735304 0 0.050034 361831459 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 21623875 21623875 2.0 1.937595 523728 523728 3.0 2.81668 10408 10408 4.0 3.640906 885 885 5.0 4.413697 483 483 6.0 5.138261 314 314 7.0 5.81761 210 210 8.0 6.454563 199 199 9.0 7.051768 174 174 10.0 7.611705 129 129 11.0 8.136699 125 125 12.0 8.628931 128 128 13.0 9.090445 111 111 14.0 9.523158 114 114 15.0 9.928869 105 105 16.0 10.309261 102 102 17.0 10.665914 98 98 18.0 11.000311 65 65 19.0 11.31384 79 79 20.0 11.607803 82 82 21.0 11.883422 65 65 22.0 12.141841 75 75 23.0 12.384133 48 48 24.0 12.611305 55 55 25.0 12.8243 61 61 26.0 13.024003 43 43 27.0 13.211245 55 55 28.0 13.386801 48 48 29.0 13.551402 35 35 30.0 13.705731 42 42 31.0 13.850429 40 40 32.0 13.986097 41 41 33.0 14.113299 29 29 34.0 14.232563 27 27 35.0 14.344384 24 24 36.0 14.449227 38 38 37.0 14.547527 27 27 38.0 14.639693 22 22 39.0 14.726108 29 29 40.0 14.807129 13 13 41.0 14.883095 14 14 42.0 14.95432 29 29 43.0 15.0211 24 24 44.0 15.083713 20 20 45.0 15.142419 20 20 46.0 15.197461 24 24 47.0 15.249068 16 16 48.0 15.297454 16 16 49.0 15.342821 16 16 50.0 15.385357 22 22 51.0 15.425239 16 16 52.0 15.462631 9 9 53.0 15.497691 12 12 54.0 15.530562 15 15 55.0 15.561382 24 24 56.0 15.590279 17 17 57.0 15.617372 11 11 58.0 15.642775 16 16 59.0 15.666592 11 11 60.0 15.688923 15 15 61.0 15.709861 10 10 62.0 15.729492 13 13 63.0 15.747897 10 10 64.0 15.765155 13 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