## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2015-08-25/UA_Che_Var_1_2015-08-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2015-08-25/UA_Che_Var_1_2015-08-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2015-08-25/UA_Che_Var_1_2015-08-25.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 20 08:53:28 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	12047049	25235806	0	0	3848575	2305989	0	0.135328	129538502

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20429873	20429873
2.0	1.822988	1875511	1875511
3.0	2.500298	148658	148658
4.0	3.057717	12736	12736
5.0	3.516465	2302	2302
6.0	3.89401	1027	1027
7.0	4.204725	696	696
8.0	4.46044	502	502
9.0	4.67089	399	399
10.0	4.844089	271	271
11.0	4.986629	207	207
12.0	5.103938	179	179
13.0	5.200482	167	167
14.0	5.279936	124	124
15.0	5.345326	115	115
16.0	5.399141	110	110
17.0	5.443431	88	88
18.0	5.47988	85	85
19.0	5.509878	64	64
20.0	5.534566	54	54
21.0	5.554883	50	50
22.0	5.571605	55	55
23.0	5.585366	51	51
24.0	5.596691	40	40
25.0	5.606012	39	39
26.0	5.613683	44	44
27.0	5.619996	34	34
28.0	5.625192	33	33
29.0	5.629467	25	25
30.0	5.632986	18	18
31.0	5.635882	22	22
32.0	5.638266	26	26
33.0	5.640227	21	21
34.0	5.641842	18	18
35.0	5.64317	21	21
36.0	5.644264	18	18
37.0	5.645164	12	12
38.0	5.645904	12	12
39.0	5.646514	17	17
40.0	5.647015	13	13
41.0	5.647428	10	10
42.0	5.647768	15	15
43.0	5.648047	13	13
44.0	5.648278	14	14
45.0	5.648467	15	15
46.0	5.648623	11	11
47.0	5.648751	8	8
48.0	5.648857	8	8
49.0	5.648943	7	7
50.0	5.649015	14	14
51.0	5.649074	11	11
52.0	5.649122	4	4
53.0	5.649162	7	7
54.0	5.649195	4	4
55.0	5.649222	3	3
56.0	5.649244	4	4
57.0	5.649262	8	8
58.0	5.649277	10	10
59.0	5.64929	10	10
60.0	5.6493	7	7
61.0	5.649308	7	7
62.0	5.649315	9	9
63.0	5.649321	6	6
64.0	5.649326	8	8
65.0	5.64933	6	6
66.0	5.649333	5	5
67.0	5.649335	7	7
68.0	5.649337	8	8
69.0	5.649339	8	8
70.0	5.649341	4	4
71.0	5.649342	8	8
72.0	5.649343	3	3
73.0	5.649344	3	3
74.0	5.649344	6	6
75.0	5.649345	3	3
76.0	5.649345	4	4
77.0	5.649346	2	2
78.0	5.649346	7	7
79.0	5.649346	3	3
80.0	5.649346	6	6
81.0	5.649347	2	2
82.0	5.649347	4	4
83.0	5.649347	4	4
84.0	5.649347	1	1
85.0	5.649347	3	3
86.0	5.649347	0	0
87.0	5.649347	3	3
88.0	5.649347	0	0
89.0	5.649347	4	4
90.0	5.649347	2	2
91.0	5.649347	4	4
92.0	5.649347	2	2
93.0	5.649347	3	3
94.0	5.649347	1	1
95.0	5.649347	2	2
96.0	5.649347	1	1
97.0	5.649347	4	4
98.0	5.649347	2	2
99.0	5.649347	2	2
100.0	5.649347	3	3
101.0	0	2	2
102.0	0	4	4
105.0	0	2	2
107.0	0	1	1
108.0	0	2	2
110.0	0	1	1
111.0	0	2	2
112.0	0	1	1
113.0	0	5	5
114.0	0	5	5
115.0	0	3	3
116.0	0	1	1
117.0	0	1	1
118.0	0	1	1
120.0	0	1	1
121.0	0	2	2
122.0	0	1	1
123.0	0	1	1
124.0	0	2	2
125.0	0	1	1
126.0	0	2	2
130.0	0	1	1
131.0	0	1	1
132.0	0	1	1
134.0	0	1	1
140.0	0	1	1
144.0	0	1	1
145.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	2	2
152.0	0	1	1
156.0	0	1	1
163.0	0	1	1
165.0	0	1	1
172.0	0	1	1
177.0	0	1	1
185.0	0	1	1
186.0	0	2	2
199.0	0	1	1
201.0	0	1	1
202.0	0	1	1
207.0	0	1	1
211.0	0	1	1
215.0	0	1	1
222.0	0	1	1
225.0	0	1	1
227.0	0	1	1
228.0	0	1	1
239.0	0	1	1
249.0	0	1	1
253.0	0	1	1
271.0	0	1	1
288.0	0	1	1
291.0	0	1	1
325.0	0	1	1
357.0	0	1	1
374.0	0	1	1
390.0	0	1	1
413.0	0	1	1
427.0	0	1	1
462.0	0	1	1
464.0	0	1	1
532.0	0	1	1