## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Cal_And_4_2013-10-15/US_Cal_And_4_2013-10-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Cal_And_4_2013-10-15/US_Cal_And_4_2013-10-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Cal_And_4_2013-10-15/US_Cal_And_4_2013-10-15.mark_duplicates_report.txt 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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Jan 13 21:10:04 UTC 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
lib1	320726	2981222	0	0	30173	13097	0	0.008971	338307836

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	2923530	2923530
2.0	1.991227	12520	12520
3.0	2.973757	163	163
4.0	3.947667	37	37
5.0	4.913032	14	14
6.0	5.869928	1	1
7.0	6.818428	5	5
8.0	7.758607	2	2
9.0	8.690537	2	2
10.0	9.614291	1	1
11.0	10.529941	1	1
12.0	11.437557	0	0
13.0	12.33721	0	0
14.0	13.228971	0	0
15.0	14.112907	0	0
16.0	14.989088	0	0
17.0	15.857582	0	0
18.0	16.718457	0	0
19.0	17.571778	0	0
20.0	18.417613	0	0
21.0	19.256027	0	0
22.0	20.087086	0	0
23.0	20.910853	0	0
24.0	21.727392	0	0
25.0	22.536768	0	0
26.0	23.339043	0	0
27.0	24.134279	0	0
28.0	24.922539	0	0
29.0	25.703882	0	0
30.0	26.478371	0	0
31.0	27.246064	0	0
32.0	28.007022	0	0
33.0	28.761304	0	0
34.0	29.508968	0	0
35.0	30.250073	0	0
36.0	30.984676	0	0
37.0	31.712834	0	0
38.0	32.434603	0	0
39.0	33.15004	0	0
40.0	33.8592	0	0
41.0	34.562138	0	0
42.0	35.258909	0	0
43.0	35.949567	0	0
44.0	36.634165	0	0
45.0	37.312757	0	0
46.0	37.985396	0	0
47.0	38.652133	0	0
48.0	39.313021	0	0
49.0	39.96811	0	0
50.0	40.617452	0	0
51.0	41.261097	0	0
52.0	41.899095	0	0
53.0	42.531496	0	0
54.0	43.158348	0	0
55.0	43.779701	0	0
56.0	44.395602	0	0
57.0	45.0061	0	0
58.0	45.611241	0	0
59.0	46.211074	0	0
60.0	46.805643	0	0
61.0	47.394997	0	0
62.0	47.979179	0	0
63.0	48.558236	0	0
64.0	49.132213	0	0
65.0	49.701155	0	0
66.0	50.265104	0	0
67.0	50.824106	0	0
68.0	51.378204	0	0
69.0	51.92744	0	0
70.0	52.471858	0	0
71.0	53.011499	0	0
72.0	53.546405	0	0
73.0	54.076619	0	0
74.0	54.602181	0	0
75.0	55.123131	0	0
76.0	55.639512	0	0
77.0	56.151361	0	0
78.0	56.658721	0	0
79.0	57.161628	0	0
80.0	57.660124	0	0
81.0	58.154246	0	0
82.0	58.644033	0	0
83.0	59.129523	0	0
84.0	59.610753	0	0
85.0	60.087762	0	0
86.0	60.560585	0	0
87.0	61.02926	0	0
88.0	61.493823	0	0
89.0	61.954311	0	0
90.0	62.410758	0	0
91.0	62.863201	0	0
92.0	63.311674	0	0
93.0	63.756212	0	0
94.0	64.196851	0	0
95.0	64.633623	0	0
96.0	65.066564	0	0
97.0	65.495706	0	0
98.0	65.921083	0	0
99.0	66.342728	0	0
100.0	66.760674	0	0