## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[test.sorted.bam] OUTPUT=test.markdup.bam METRICS_FILE=test.markdup_metrics.txt REMOVE_DUPLICATES=false READ_NAME_REGEX=^(?:[^:]*:){4}([^:]+):([^:]+):([^:]+)(?::[^:]*) OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.TTWv5IRBtJ] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_DUP_STRATEGY=FLOW_QUALITY_SUM_STRATEGY FLOW_USE_END_IN_UNPAIRED_READS=false FLOW_USE_UNPAIRED_CLIPPED_END=false FLOW_UNPAIRED_END_UNCERTAINTY=0 FLOW_UNPAIRED_START_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 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu May 14 22:40:35 UTC 2026
## 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
test 16 244701 1339 130 0 15622 14589 0.063839 25553215
## HISTOGRAM java.lang.Double
BIN CoverageMult all_sets optical_sets non_optical_sets
1.0 1.063097 214429 0 228063
2.0 2.116061 13753 12936 1006
3.0 3.158991 832 735 6
4.0 4.191981 57 53 2
5.0 5.215126 6 6 1
6.0 6.22852 2 0 1
7.0 7.232256 0 0 0
8.0 8.226426 0 0 0
9.0 9.211121 0 0 0
10.0 10.186432 0 0 0
11.0 11.152447 0 0 0
12.0 12.109256 0 0 0
13.0 13.056946 0 0 0
14.0 13.995605 0 0 0
15.0 14.925317 0 0 0
16.0 15.846169 0 0 0
17.0 16.758245 0 0 0
18.0 17.661628 0 0 0
19.0 18.556401 0 0 0
20.0 19.442647 0 0 0
21.0 20.320447 0 0 0
22.0 21.189881 0 0 0
23.0 22.051029 0 0 0
24.0 22.90397 0 0 0
25.0 23.748782 0 0 0
26.0 24.585542 0 0 0
27.0 25.414328 0 0 0
28.0 26.235215 0 0 0
29.0 27.048279 0 0 0
30.0 27.853593 0 0 0
31.0 28.651233 0 0 0
32.0 29.441271 0 0 0
33.0 30.22378 0 0 0
34.0 30.998831 0 0 0
35.0 31.766495 0 0 0
36.0 32.526843 0 0 0
37.0 33.279945 0 0 0
38.0 34.02587 0 0 0
39.0 34.764685 0 0 0
40.0 35.496459 0 0 0
41.0 36.221259 0 0 0
42.0 36.939152 0 0 0
43.0 37.650202 0 0 0
44.0 38.354476 0 0 0
45.0 39.052038 0 0 0
46.0 39.742952 0 0 0
47.0 40.427281 0 0 0
48.0 41.105088 0 0 0
49.0 41.776436 0 0 0
50.0 42.441385 0 0 0
51.0 43.099997 0 0 0
52.0 43.752332 0 0 0
53.0 44.39845 0 0 0
54.0 45.03841 0 0 0
55.0 45.672271 0 0 0
56.0 46.300092 0 0 0
57.0 46.921928 0 0 0
58.0 47.537839 0 0 0
59.0 48.147879 0 0 0
60.0 48.752106 0 0 0
61.0 49.350574 0 0 0
62.0 49.943338 0 0 0
63.0 50.530453 0 0 0
64.0 51.111973 0 0 0
65.0 51.687951 0 0 0
66.0 52.258439 0 0 0
67.0 52.82349 0 0 0
68.0 53.383156 0 0 0
69.0 53.937488 0 0 0
70.0 54.486537 0 0 0
71.0 55.030354 0 0 0
72.0 55.568988 0 0 0
73.0 56.102488 0 0 0
74.0 56.630904 0 0 0
75.0 57.154283 0 0 0
76.0 57.672675 0 0 0
77.0 58.186126 0 0 0
78.0 58.694684 0 0 0
79.0 59.198395 0 0 0
80.0 59.697305 0 0 0
81.0 60.191461 0 0 0
82.0 60.680907 0 0 0
83.0 61.165689 0 0 0
84.0 61.64585 0 0 0
85.0 62.121435 0 0 0
86.0 62.592488 0 0 0
87.0 63.059051 0 0 0
88.0 63.521168 0 0 0
89.0 63.97888 0 0 0
90.0 64.432231 0 0 0
91.0 64.88126 0 0 0
92.0 65.326011 0 0 0
93.0 65.766522 0 0 0
94.0 66.202836 0 0 0
95.0 66.634991 0 0 0
96.0 67.063027 0 0 0
97.0 67.486985 0 0 0
98.0 67.906901 0 0 0
99.0 68.322816 0 0 0
100.0 68.734767 0 0 0