## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2015-08-01/CH_Vau_Cha_1_2015-08-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2015-08-01/CH_Vau_Cha_1_2015-08-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2015-08-01/CH_Vau_Cha_1_2015-08-01.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 08:56:14 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	6655122	28872381	0	0	2793388	2942348	0	0.134753	131860891

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22963156	22963156
2.0	1.803353	2306576	2306576
3.0	2.448729	208159	208159
4.0	2.967194	20014	20014
5.0	3.383705	2940	2940
6.0	3.71831	940	940
7.0	3.987116	525	525
8.0	4.203062	429	429
9.0	4.376543	278	278
10.0	4.515909	252	252
11.0	4.62787	220	220
12.0	4.717814	180	180
13.0	4.79007	150	150
14.0	4.848118	131	131
15.0	4.894751	148	148
16.0	4.932213	118	118
17.0	4.962309	112	112
18.0	4.986486	120	120
19.0	5.005909	95	95
20.0	5.021513	73	73
21.0	5.034048	81	81
22.0	5.044118	75	75
23.0	5.052208	93	93
24.0	5.058707	61	61
25.0	5.063928	68	68
26.0	5.068122	70	70
27.0	5.071492	69	69
28.0	5.074199	55	55
29.0	5.076374	51	51
30.0	5.07812	54	54
31.0	5.079524	45	45
32.0	5.080651	46	46
33.0	5.081557	35	35
34.0	5.082285	46	46
35.0	5.082869	35	35
36.0	5.083339	43	43
37.0	5.083716	34	34
38.0	5.084019	37	37
39.0	5.084263	35	35
40.0	5.084458	20	20
41.0	5.084615	21	21
42.0	5.084742	16	16
43.0	5.084843	28	28
44.0	5.084925	31	31
45.0	5.08499	24	24
46.0	5.085043	36	36
47.0	5.085085	15	15
48.0	5.085119	25	25
49.0	5.085146	31	31
50.0	5.085168	23	23
51.0	5.085185	16	16
52.0	5.0852	28	28
53.0	5.085211	14	14
54.0	5.08522	12	12
55.0	5.085227	11	11
56.0	5.085233	18	18
57.0	5.085238	14	14
58.0	5.085242	11	11
59.0	5.085245	16	16
60.0	5.085247	18	18
61.0	5.085249	7	7
62.0	5.085251	15	15
63.0	5.085252	18	18
64.0	5.085253	8	8
65.0	5.085254	12	12
66.0	5.085255	13	13
67.0	5.085255	19	19
68.0	5.085256	16	16
69.0	5.085256	13	13
70.0	5.085256	4	4
71.0	5.085256	9	9
72.0	5.085257	8	8
73.0	5.085257	12	12
74.0	5.085257	7	7
75.0	5.085257	11	11
76.0	5.085257	12	12
77.0	5.085257	7	7
78.0	5.085257	4	4
79.0	5.085257	11	11
80.0	5.085257	8	8
81.0	5.085257	9	9
82.0	5.085257	6	6
83.0	5.085257	9	9
84.0	5.085257	6	6
85.0	5.085257	5	5
86.0	5.085257	2	2
87.0	5.085257	10	10
88.0	5.085257	7	7
89.0	5.085257	5	5
90.0	5.085257	6	6
91.0	5.085257	6	6
92.0	5.085257	5	5
93.0	5.085257	1	1
94.0	5.085257	5	5
95.0	5.085257	5	5
96.0	5.085257	6	6
97.0	5.085257	7	7
98.0	5.085257	4	4
99.0	5.085257	4	4
100.0	5.085257	5	5
101.0	0	5	5
102.0	0	8	8
103.0	0	7	7
104.0	0	1	1
105.0	0	6	6
106.0	0	2	2
107.0	0	5	5
108.0	0	5	5
109.0	0	1	1
110.0	0	4	4
111.0	0	4	4
112.0	0	6	6
113.0	0	3	3
114.0	0	12	12
115.0	0	5	5
116.0	0	3	3
117.0	0	6	6
118.0	0	2	2
119.0	0	3	3
120.0	0	3	3
122.0	0	1	1
123.0	0	1	1
124.0	0	4	4
125.0	0	1	1
126.0	0	5	5
127.0	0	3	3
128.0	0	4	4
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
133.0	0	3	3
134.0	0	2	2
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
139.0	0	2	2
140.0	0	2	2
141.0	0	1	1
142.0	0	1	1
143.0	0	5	5
144.0	0	2	2
145.0	0	2	2
146.0	0	4	4
147.0	0	1	1
148.0	0	1	1
150.0	0	1	1
151.0	0	3	3
152.0	0	2	2
153.0	0	3	3
154.0	0	1	1
155.0	0	1	1
156.0	0	4	4
157.0	0	1	1
160.0	0	2	2
161.0	0	4	4
162.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	2	2
170.0	0	2	2
173.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
180.0	0	1	1
182.0	0	3	3
183.0	0	1	1
184.0	0	1	1
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	2	2
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
209.0	0	2	2
211.0	0	1	1
215.0	0	2	2
223.0	0	1	1
224.0	0	1	1
227.0	0	1	1
228.0	0	2	2
231.0	0	1	1
243.0	0	1	1
245.0	0	2	2
248.0	0	1	1
249.0	0	1	1
251.0	0	1	1
261.0	0	1	1
263.0	0	1	1
268.0	0	1	1
273.0	0	1	1
275.0	0	1	1
278.0	0	1	1
295.0	0	1	1
300.0	0	1	1
305.0	0	1	1
308.0	0	1	1
311.0	0	1	1
314.0	0	1	1
319.0	0	1	1
320.0	0	1	1
342.0	0	1	1
343.0	0	1	1
357.0	0	1	1
394.0	0	1	1
412.0	0	1	1
423.0	0	1	1
427.0	0	1	1
474.0	0	1	1
488.0	0	1	1