## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2016-10-23/GB_Nor_Mar_1_2016-10-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2016-10-23/GB_Nor_Mar_1_2016-10-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2016-10-23/GB_Nor_Mar_1_2016-10-23.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 09:38:43 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 39275666 15348331 0 0 11185606 1408484 0 0.200116 78427381 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 12515433 12515433 2.0 1.822258 914320 914320 3.0 2.498366 77006 77006 4.0 3.054301 9595 9595 5.0 3.511423 2985 2985 6.0 3.887296 1792 1792 7.0 4.196359 1225 1225 8.0 4.45049 913 913 9.0 4.65945 671 671 10.0 4.83127 545 545 11.0 4.97255 416 416 12.0 5.088718 359 359 13.0 5.184239 291 291 14.0 5.262781 246 246 15.0 5.327364 218 218 16.0 5.380467 172 172 17.0 5.424131 132 132 18.0 5.460035 134 134 19.0 5.489557 144 144 20.0 5.513832 126 126 21.0 5.533792 108 108 22.0 5.550204 121 121 23.0 5.563699 96 96 24.0 5.574795 82 82 25.0 5.58392 81 81 26.0 5.591422 72 72 27.0 5.597591 73 73 28.0 5.602663 77 77 29.0 5.606834 81 81 30.0 5.610264 70 70 31.0 5.613084 77 77 32.0 5.615403 58 58 33.0 5.617309 69 69 34.0 5.618877 43 43 35.0 5.620166 73 73 36.0 5.621226 56 56 37.0 5.622097 64 64 38.0 5.622814 49 49 39.0 5.623403 40 40 40.0 5.623888 57 57 41.0 5.624286 46 46 42.0 5.624614 46 46 43.0 5.624883 29 29 44.0 5.625105 50 50 45.0 5.625287 39 39 46.0 5.625436 39 39 47.0 5.62556 35 35 48.0 5.625661 40 40 49.0 5.625744 31 31 50.0 5.625813 30 30 51.0 5.625869 28 28 52.0 5.625915 32 32 53.0 5.625953 40 40 54.0 5.625984 30 30 55.0 5.62601 19 19 56.0 5.626031 28 28 57.0 5.626049 24 24 58.0 5.626063 29 29 59.0 5.626075 19 19 60.0 5.626085 20 20 61.0 5.626092 16 16 62.0 5.626099 20 20 63.0 5.626104 16 16 64.0 5.626109 22 22 65.0 5.626112 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