## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-07-20/US_Mas_Lan_1_2014-07-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-07-20/US_Mas_Lan_1_2014-07-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-07-20/US_Mas_Lan_1_2014-07-20.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 20:28:30 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 1687735 51578629 0 0 836247 14450521 0 0.283631 73906497 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 25309366 25309366 2.0 1.497634 7770960 7770960 3.0 1.745274 2091455 2091455 4.0 1.868508 504198 504198 5.0 1.929833 116508 116508 6.0 1.960351 28393 28393 7.0 1.975537 8737 8737 8.0 1.983095 3760 3760 9.0 1.986855 2223 2223 10.0 1.988727 1521 1521 11.0 1.989658 1090 1090 12.0 1.990122 828 828 13.0 1.990352 684 684 14.0 1.990467 591 591 15.0 1.990524 442 442 16.0 1.990553 346 346 17.0 1.990567 287 287 18.0 1.990574 270 270 19.0 1.990577 212 212 20.0 1.990579 163 163 21.0 1.99058 181 181 22.0 1.99058 163 163 23.0 1.990581 112 112 24.0 1.990581 112 112 25.0 1.990581 129 129 26.0 1.990581 100 100 27.0 1.990581 103 103 28.0 1.990581 77 77 29.0 1.990581 75 75 30.0 1.990581 61 61 31.0 1.990581 66 66 32.0 1.990581 63 63 33.0 1.990581 61 61 34.0 1.990581 48 48 35.0 1.990581 60 60 36.0 1.990581 46 46 37.0 1.990581 49 49 38.0 1.990581 48 48 39.0 1.990581 39 39 40.0 1.990581 42 42 41.0 1.990581 48 48 42.0 1.990581 34 34 43.0 1.990581 31 31 44.0 1.990581 36 36 45.0 1.990581 30 30 46.0 1.990581 30 30 47.0 1.990581 30 30 48.0 1.990581 31 31 49.0 1.990581 30 30 50.0 1.990581 15 15 51.0 1.990581 12 12 52.0 1.990581 29 29 53.0 1.990581 21 21 54.0 1.990581 16 16 55.0 1.990581 25 25 56.0 1.990581 13 13 57.0 1.990581 20 20 58.0 1.990581 23 23 59.0 1.990581 24 24 60.0 1.990581 13 13 61.0 1.990581 11 11 62.0 1.990581 13 13 63.0 1.990581 11 11 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