## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2013-09-03/US_Cal_Sto_1_2013-09-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2013-09-03/US_Cal_Sto_1_2013-09-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2013-09-03/US_Cal_Sto_1_2013-09-03.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 18:23:50 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 6287805 39876092 0 0 2052789 1243953 0 0.052774 625770641 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 36935594 36935594 2.0 1.938265 706041 706041 3.0 2.818605 26366 26366 4.0 3.644598 5848 5848 5.0 4.419598 2607 2607 6.0 5.146752 1367 1367 7.0 5.829016 888 888 8.0 6.46916 596 596 9.0 7.069784 450 450 10.0 7.633329 332 332 11.0 8.162083 310 310 12.0 8.658195 253 253 13.0 9.123678 214 214 14.0 9.560425 217 217 15.0 9.97021 184 184 16.0 10.354696 142 142 17.0 10.715445 152 152 18.0 11.053924 110 110 19.0 11.371507 93 93 20.0 11.669483 84 84 21.0 11.949064 67 67 22.0 12.211385 74 74 23.0 12.457512 59 59 24.0 12.688444 46 46 25.0 12.905119 56 56 26.0 13.108417 49 49 27.0 13.299165 47 47 28.0 13.478137 34 34 29.0 13.64606 48 48 30.0 13.803617 30 30 31.0 13.951446 34 34 32.0 14.09015 23 23 33.0 14.22029 25 25 34.0 14.342396 36 36 35.0 14.456964 27 27 36.0 14.564459 35 35 37.0 14.665318 41 41 38.0 14.75995 25 25 39.0 14.84874 32 32 40.0 14.932048 32 32 41.0 15.010214 29 29 42.0 15.083554 26 26 43.0 15.152366 28 28 44.0 15.21693 18 18 45.0 15.277508 17 17 46.0 15.334347 16 16 47.0 15.387676 24 24 48.0 15.437714 26 26 49.0 15.484662 21 21 50.0 15.528711 15 15 51.0 15.570042 29 29 52.0 15.60882 13 13 53.0 15.645205 24 24 54.0 15.679344 13 13 55.0 15.711375 22 22 56.0 15.741428 19 19 57.0 15.769627 18 18 58.0 15.796084 16 16 59.0 15.820908 21 21 60.0 15.844199 15 15 61.0 15.866053 18 18 62.0 15.886557 17 17 63.0 15.905796 24 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