## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-IgG_R1.target.markdup.sorted.bam --OUTPUT DE-IgG_R1.target.dedup.bam --METRICS_FILE DE-IgG_R1.target.dedup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES true --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --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 --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Jun 15 14:48:59 GMT 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 Unknown Library 0 7395273 0 0 0 120857 1062 0.016342 225728208 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000141 7155270 0 7156283 2.0 1.968047 117582 1060 116618 3.0 2.904756 1487 1 1438 4.0 3.811274 50 0 50 5.0 4.688574 15 0 15 6.0 5.537598 4 0 4 7.0 6.359257 0 0 0 8.0 7.154433 4 0 4 9.0 7.92398 1 0 1 10.0 8.668724 1 0 1 11.0 9.389464 1 0 1 12.0 10.086973 0 0 0 13.0 10.762001 0 0 0 14.0 11.415273 0 0 0 15.0 12.047488 0 0 0 16.0 12.659327 0 0 0 17.0 13.251446 1 0 1 18.0 13.82448 0 0 0 19.0 14.379044 0 0 0 20.0 14.915735 0 0 0 21.0 15.435127 0 0 0 22.0 15.937779 0 0 0 23.0 16.42423 0 0 0 24.0 16.895002 0 0 0 25.0 17.350601 0 0 0 26.0 17.791515 0 0 0 27.0 18.218218 0 0 0 28.0 18.631168 0 0 0 29.0 19.030808 0 0 0 30.0 19.417568 0 0 0 31.0 19.791862 0 0 0 32.0 20.154092 0 0 0 33.0 20.504647 0 0 0 34.0 20.843903 0 0 0 35.0 21.172224 0 0 0 36.0 21.489964 0 0 0 37.0 21.797462 0 0 0 38.0 22.09505 0 0 0 39.0 22.383046 0 0 0 40.0 22.661759 0 0 0 41.0 22.93149 0 0 0 42.0 23.192526 0 0 0 43.0 23.44515 0 0 0 44.0 23.68963 0 0 0 45.0 23.926232 0 0 0 46.0 24.155207 0 0 0 47.0 24.376802 0 0 0 48.0 24.591255 0 0 0 49.0 24.798795 0 0 0 50.0 24.999647 0 0 0 51.0 25.194025 0 0 0 52.0 25.382138 0 0 0 53.0 25.564187 0 0 0 54.0 25.74037 0 0 0 55.0 25.910873 0 0 0 56.0 26.075882 0 0 0 57.0 26.235571 0 0 0 58.0 26.390114 0 0 0 59.0 26.539676 0 0 0 60.0 26.684417 0 0 0 61.0 26.824493 0 0 0 62.0 26.960055 0 0 0 63.0 27.091247 0 0 0 64.0 27.21821 0 0 0 65.0 27.341082 0 0 0 66.0 27.459993 0 0 0 67.0 27.575071 0 0 0 68.0 27.686441 0 0 0 69.0 27.79422 0 0 0 70.0 27.898527 0 0 0 71.0 27.999471 0 0 0 72.0 28.097161 0 0 0 73.0 28.191703 0 0 0 74.0 28.283198 0 0 0 75.0 28.371744 0 0 0 76.0 28.457436 0 0 0 77.0 28.540366 0 0 0 78.0 28.620623 0 0 0 79.0 28.698293 0 0 0 80.0 28.77346 0 0 0 81.0 28.846204 0 0 0 82.0 28.916603 0 0 0 83.0 28.984734 0 0 0 84.0 29.050669 0 0 0 85.0 29.114478 0 0 0 86.0 29.176231 0 0 0 87.0 29.235993 0 0 0 88.0 29.29383 0 0 0 89.0 29.349802 0 0 0 90.0 29.40397 0 0 0 91.0 29.456392 0 0 0 92.0 29.507125 0 0 0 93.0 29.556222 0 0 0 94.0 29.603737 0 0 0 95.0 29.649721 0 0 0 96.0 29.694222 0 0 0 97.0 29.737289 0 0 0 98.0 29.778968 0 0 0 99.0 29.819304 0 0 0 100.0 29.858339 0 0 0