## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-08-09/UA_Kie_Kyi_1_2014-08-09.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-08-09/UA_Kie_Kyi_1_2014-08-09.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-08-09/UA_Kie_Kyi_1_2014-08-09.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 16:54:51 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 18617018 11936140 0 0 4023991 599256 0 0.122913 114860673 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 10752281 10752281 2.0 1.901299 229005 229005 3.0 2.713638 5398 5398 4.0 3.445799 1018 1018 5.0 4.105695 577 577 6.0 4.700458 375 375 7.0 5.236517 268 268 8.0 5.719667 235 235 9.0 6.155129 208 208 10.0 6.54761 158 158 11.0 6.901353 150 150 12.0 7.220182 125 125 13.0 7.507541 105 105 14.0 7.766538 110 110 15.0 7.999972 92 92 16.0 8.210365 69 69 17.0 8.399992 68 68 18.0 8.570903 89 89 19.0 8.724945 66 66 20.0 8.863782 62 62 21.0 8.988917 57 57 22.0 9.1017 57 57 23.0 9.203351 50 50 24.0 9.29497 41 41 25.0 9.377545 64 64 26.0 9.451971 55 55 27.0 9.51905 28 28 28.0 9.579508 44 44 29.0 9.634 32 32 30.0 9.683112 37 37 31.0 9.727378 30 30 32.0 9.767274 33 33 33.0 9.803233 26 26 34.0 9.835642 27 27 35.0 9.864853 24 24 36.0 9.89118 29 29 37.0 9.914909 32 32 38.0 9.936296 30 30 39.0 9.955572 26 26 40.0 9.972945 19 19 41.0 9.988603 23 23 42.0 10.002716 25 25 43.0 10.015437 29 29 44.0 10.026901 19 19 45.0 10.037234 23 23 46.0 10.046547 19 19 47.0 10.054941 15 15 48.0 10.062507 19 19 49.0 10.069325 17 17 50.0 10.075471 15 15 51.0 10.08101 9 9 52.0 10.086003 12 12 53.0 10.090502 17 17 54.0 10.094558 17 17 55.0 10.098213 8 8 56.0 10.101507 12 12 57.0 10.104477 13 13 58.0 10.107153 11 11 59.0 10.109565 10 10 60.0 10.111739 8 8 61.0 10.113698 13 13 62.0 10.115464 17 17 63.0 10.117056 10 10 64.0 10.118491 8 8 65.0 10.119784 9 9 66.0 10.120949 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