## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mic_Ben_1_2014-07-26/US_Mic_Ben_1_2014-07-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mic_Ben_1_2014-07-26/US_Mic_Ben_1_2014-07-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mic_Ben_1_2014-07-26/US_Mic_Ben_1_2014-07-26.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 21:21:57 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 865313 61827617 0 0 445128 9504482 0 0.156232 179911919 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 43031064 43031064 2.0 1.709174 6785529 6785529 3.0 2.212101 962976 962976 4.0 2.568763 129732 129732 5.0 2.821699 19777 19777 6.0 3.001075 4841 4841 7.0 3.128283 2296 2296 8.0 3.218496 1527 1527 9.0 3.282472 1101 1101 10.0 3.327843 845 845 11.0 3.360018 620 620 12.0 3.382836 526 526 13.0 3.399018 436 436 14.0 3.410494 350 350 15.0 3.418632 297 297 16.0 3.424404 261 261 17.0 3.428497 231 231 18.0 3.431399 207 207 19.0 3.433458 173 173 20.0 3.434918 174 174 21.0 3.435953 169 169 22.0 3.436687 129 129 23.0 3.437208 101 101 24.0 3.437577 109 109 25.0 3.437839 72 72 26.0 3.438025 94 94 27.0 3.438156 89 89 28.0 3.43825 77 77 29.0 3.438316 71 71 30.0 3.438363 57 57 31.0 3.438396 65 65 32.0 3.43842 45 45 33.0 3.438437 58 58 34.0 3.438448 57 57 35.0 3.438457 37 37 36.0 3.438463 43 43 37.0 3.438467 33 33 38.0 3.43847 38 38 39.0 3.438472 38 38 40.0 3.438474 38 38 41.0 3.438475 40 40 42.0 3.438476 31 31 43.0 3.438476 22 22 44.0 3.438477 22 22 45.0 3.438477 27 27 46.0 3.438477 25 25 47.0 3.438477 27 27 48.0 3.438477 26 26 49.0 3.438477 24 24 50.0 3.438477 33 33 51.0 3.438477 23 23 52.0 3.438477 29 29 53.0 3.438477 17 17 54.0 3.438477 17 17 55.0 3.438477 24 24 56.0 3.438477 20 20 57.0 3.438477 14 14 58.0 3.438477 12 12 59.0 3.438477 18 18 60.0 3.438477 17 17 61.0 3.438477 21 21 62.0 3.438477 12 12 63.0 3.438477 11 11 64.0 3.438477 12 12 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