## net.sf.picard.metrics.StringHeader # net.sf.picard.sam.EstimateLibraryComplexity INPUT=[sigmoid_colon-ENCSR355SGJ-rep1-1.2x36mers.hg38-no-haps.unique.nochrM.bam] OUTPUT=sigmoid_colon-ENCSR355SGJ-rep1-1.2x36mers.hg38-no-haps.unique.nochrM.est_lib_complex_metrics.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false ## net.sf.picard.metrics.StringHeader # Started on: Mon Nov 25 10:30:53 PST 2019 ## METRICS CLASS net.sf.picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown 0 51885085 0 0 7304132 6302491 0.140775 1021933911 ## HISTOGRAM java.lang.Integer duplication_group_count Unknown 1 38358614 2 5316000 3 768563 4 115001 5 17980 6 2987 7 690 8 267 9 130 10 111 11 80 12 69 13 60 14 33 15 50 16 42 17 29 18 16 19 21 20 23 21 14 22 17 23 13 24 13 25 12 26 17 27 12 28 12 29 8 30 4 31 5 32 4 33 5 34 5 35 7 36 2 37 1 38 3 39 3 40 2 41 4 42 3 43 3 44 3 47 1 48 1 49 2 50 2 52 2 53 3 55 3 56 1 57 1 59 2 62 2 63 1 64 1 66 1 69 1 78 1 80 1 81 1 83 1 84 1 86 1 93 1 110 1 126 1 170 1