## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2014-08-20/UA_Pol_Pyr_1_2014-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2014-08-20/UA_Pol_Pyr_1_2014-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2014-08-20/UA_Pol_Pyr_1_2014-08-20.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 18:07:14 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 19986086 16597944 0 0 4118319 718612 0 0.104463 186109714 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 15122449 15122449 2.0 1.914678 345233 345233 3.0 2.751313 8074 8074 4.0 3.516564 1162 1162 5.0 4.216522 675 675 6.0 4.856758 463 463 7.0 5.442368 348 348 8.0 5.978012 244 244 9.0 6.467953 214 214 10.0 6.916092 183 183 11.0 7.325994 134 134 12.0 7.700923 117 117 13.0 8.043861 116 116 14.0 8.35754 109 109 15.0 8.644454 100 100 16.0 8.906888 96 96 17.0 9.146931 78 78 18.0 9.366493 72 72 19.0 9.567321 69 69 20.0 9.751014 59 59 21.0 9.919034 54 54 22.0 10.072718 58 58 23.0 10.213289 44 44 24.0 10.341866 43 43 25.0 10.459473 47 47 26.0 10.567046 50 50 27.0 10.66544 40 40 28.0 10.755439 35 35 29.0 10.837758 33 33 30.0 10.913055 36 36 31.0 10.981926 34 34 32.0 11.044922 34 34 33.0 11.102542 36 36 34.0 11.155246 29 29 35.0 11.203454 23 23 36.0 11.247548 22 22 37.0 11.28788 33 33 38.0 11.324771 30 30 39.0 11.358514 24 24 40.0 11.389378 18 18 41.0 11.417608 24 24 42.0 11.44343 31 31 43.0 11.467049 16 16 44.0 11.488653 23 23 45.0 11.508413 12 12 46.0 11.526487 20 20 47.0 11.543019 11 11 48.0 11.558141 14 14 49.0 11.571972 18 18 50.0 11.584624 17 17 51.0 11.596196 15 15 52.0 11.60678 14 14 53.0 11.616461 11 11 54.0 11.625317 15 15 55.0 11.633417 13 13 56.0 11.640825 14 14 57.0 11.647602 16 16 58.0 11.6538 12 12 59.0 11.65947 12 12 60.0 11.664655 19 19 61.0 11.669399 12 12 62.0 11.673737 10 10 63.0 11.677706 9 9 64.0 11.681336 10 10 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