## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT H3K36me2_R1.target.filtered.sorted.bam --OUTPUT H3K36me2_R1.target.markdup.bam --METRICS_FILE H3K36me2_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --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: Fri May 26 22:06:12 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 13532696 0 0 0 291804 2381 0.021563 311739828 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000172 12955115 0 12957366 2.0 1.957856 280688 2381 278562 3.0 2.874855 4763 0 4643 4.0 3.752899 196 0 191 5.0 4.593643 61 0 61 6.0 5.39867 28 0 28 7.0 6.169499 12 0 12 8.0 6.907581 6 0 6 9.0 7.614309 4 0 4 10.0 8.291014 3 0 3 11.0 8.938972 1 0 1 12.0 9.559403 3 0 3 13.0 10.153478 1 0 1 14.0 10.722315 0 0 0 15.0 11.266987 2 0 2 16.0 11.788521 3 0 3 17.0 12.287899 1 0 1 18.0 12.766063 0 0 0 19.0 13.223914 0 0 0 20.0 13.662315 1 0 1 21.0 14.082091 1 0 1 22.0 14.484035 0 0 0 23.0 14.868904 0 0 0 24.0 15.237423 0 0 0 25.0 15.590287 0 0 0 26.0 15.928161 0 0 0 27.0 16.251681 0 0 0 28.0 16.561457 1 0 1 29.0 16.858074 0 0 0 30.0 17.14209 0 0 0 31.0 17.414041 1 0 1 32.0 17.674439 0 0 0 33.0 17.923775 0 0 0 34.0 18.162518 0 0 0 35.0 18.391119 0 0 0 36.0 18.61001 0 0 0 37.0 18.819601 0 0 0 38.0 19.020288 0 0 0 39.0 19.21245 0 0 0 40.0 19.396449 0 0 0 41.0 19.572631 0 0 0 42.0 19.741329 0 0 0 43.0 19.90286 0 0 0 44.0 20.057529 0 0 0 45.0 20.205628 0 0 0 46.0 20.347435 0 0 0 47.0 20.483218 0 0 0 48.0 20.613232 0 0 0 49.0 20.737724 0 0 0 50.0 20.856926 0 0 0 51.0 20.971065 0 0 0 52.0 21.080355 0 0 0 53.0 21.185003 0 0 0 54.0 21.285204 0 0 0 55.0 21.381149 0 0 0 56.0 21.473019 0 0 0 57.0 21.560985 0 0 0 58.0 21.645214 0 0 0 59.0 21.725866 0 0 0 60.0 21.803091 0 0 0 61.0 21.877035 0 0 0 62.0 21.947838 0 0 0 63.0 22.015634 0 0 0 64.0 22.080549 0 0 0 65.0 22.142707 0 0 0 66.0 22.202224 0 0 0 67.0 22.259212 0 0 0 68.0 22.31378 0 0 0 69.0 22.36603 0 0 0 70.0 22.41606 0 0 0 71.0 22.463964 0 0 0 72.0 22.509834 0 0 0 73.0 22.553755 0 0 0 74.0 22.59581 0 0 0 75.0 22.636078 0 0 0 76.0 22.674636 0 0 0 77.0 22.711556 0 0 0 78.0 22.746908 0 0 0 79.0 22.780757 0 0 0 80.0 22.813169 0 0 0 81.0 22.844204 0 0 0 82.0 22.87392 0 0 0 83.0 22.902374 0 0 0 84.0 22.929619 0 0 0 85.0 22.955707 0 0 0 86.0 22.980687 0 0 0 87.0 23.004605 0 0 0 88.0 23.027508 0 0 0 89.0 23.049437 0 0 0 90.0 23.070435 0 0 0 91.0 23.090541 0 0 0 92.0 23.109792 0 0 0 93.0 23.128226 0 0 0 94.0 23.145877 0 0 0 95.0 23.162778 0 0 0 96.0 23.178961 0 0 0 97.0 23.194456 0 0 0 98.0 23.209293 0 0 0 99.0 23.2235 0 0 0 100.0 23.237103 0 0 0 206.0 0 1 0 1