## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[sorted.bam] OUTPUT=sorted.dedup.bam METRICS_FILE=picard_dups.log 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 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 READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 08 15:04:18 PDT 2025

## 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	200526	10427827	192662	0	64537	1187152	140713	0.115825	47073647

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.01222	8247392	0	8353699
2.0	1.823311	848596	124484	769099
3.0	2.473236	119209	6627	98216
4.0	2.994021	18625	756	13991
5.0	3.411325	3659	128	2735
6.0	3.74571	1165	33	1006
7.0	4.013653	551	5	493
8.0	4.228355	356	0	336
9.0	4.400395	208	0	209
10.0	4.538251	172	0	172
11.0	4.648714	140	0	124
12.0	4.737229	87	0	88
13.0	4.808155	68	0	69
14.0	4.864988	63	0	59
15.0	4.910529	47	0	47
16.0	4.94702	33	0	33
17.0	4.976261	34	0	29
18.0	4.999691	24	0	28
19.0	5.018466	18	0	19
20.0	5.03351	24	0	20
21.0	5.045565	24	0	25
22.0	5.055224	23	0	23
23.0	5.062965	13	0	17
24.0	5.069167	14	0	11
25.0	5.074137	8	0	9
26.0	5.078119	9	0	5
27.0	5.08131	7	0	9
28.0	5.083867	6	0	7
29.0	5.085916	8	0	7
30.0	5.087558	7	0	6
31.0	5.088873	5	0	5
32.0	5.089927	6	0	5
33.0	5.090772	2	0	3
34.0	5.091449	5	0	5
35.0	5.091991	3	0	5
36.0	5.092426	3	0	0
37.0	5.092774	2	0	3
38.0	5.093053	2	0	1
39.0	5.093277	4	0	4
40.0	5.093456	2	0	3
41.0	5.093599	1	0	1
42.0	5.093714	0	0	0
43.0	5.093807	1	0	2
44.0	5.093881	3	0	2
45.0	5.09394	1	0	0
46.0	5.093987	2	0	3
47.0	5.094025	1	0	0
48.0	5.094056	2	0	3
49.0	5.09408	2	0	2
50.0	5.0941	2	0	2
51.0	5.094115	1	0	0
52.0	5.094128	0	0	0
53.0	5.094138	0	0	0
54.0	5.094146	2	0	2
55.0	5.094152	0	0	0
56.0	5.094158	2	0	2
57.0	5.094162	2	0	3
58.0	5.094165	1	0	0
59.0	5.094168	1	0	1
60.0	5.09417	1	0	2
61.0	5.094172	0	0	1
62.0	5.094173	1	0	0
63.0	5.094174	2	0	1
64.0	5.094175	2	0	2
65.0	5.094176	1	0	1
66.0	5.094176	0	0	0
67.0	5.094177	1	0	2
68.0	5.094177	1	0	1
69.0	5.094177	0	0	0
70.0	5.094177	1	0	0
71.0	5.094178	0	0	0
72.0	5.094178	0	0	0
73.0	5.094178	0	0	1
74.0	5.094178	1	0	1
75.0	5.094178	1	0	0
76.0	5.094178	0	0	0
77.0	5.094178	1	0	1
78.0	5.094178	0	0	1
79.0	5.094178	1	0	0
80.0	5.094178	0	0	0
81.0	5.094178	0	0	0
82.0	5.094178	1	0	1
83.0	5.094178	0	0	0
84.0	5.094178	1	0	1
85.0	5.094178	0	0	0
86.0	5.094178	0	0	0
87.0	5.094178	1	0	1
88.0	5.094178	0	0	0
89.0	5.094178	0	0	0
90.0	5.094178	0	0	0
91.0	5.094178	0	0	0
92.0	5.094178	0	0	0
93.0	5.094178	0	0	0
94.0	5.094178	0	0	0
95.0	5.094178	0	0	1
96.0	5.094178	1	0	0
97.0	5.094178	0	0	0
98.0	5.094178	0	0	0
99.0	5.094178	0	0	0
100.0	5.094178	0	0	0
102.0	0	0	0	1
105.0	0	1	0	0
106.0	0	0	0	1
108.0	0	1	0	0
110.0	0	1	0	1
113.0	0	0	0	1
118.0	0	1	0	0
163.0	0	1	0	1
169.0	0	0	0	1
172.0	0	1	0	0
232.0	0	0	0	1
237.0	0	1	0	0
251.0	0	0	0	1
254.0	0	1	0	0
293.0	0	0	0	1
296.0	0	1	0	0