## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2016-08-12/FR_Ess_Vil_1_2016-08-12.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2016-08-12/FR_Ess_Vil_1_2016-08-12.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2016-08-12/FR_Ess_Vil_1_2016-08-12.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 08:56:45 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	29980249	13725724	0	0	7706319	1125759	0	0.173386	79034201

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11422907	11422907
2.0	1.840576	801528	801528
3.0	2.547143	62231	62231
4.0	3.141067	6728	6728
5.0	3.640305	1931	1931
6.0	4.059952	1088	1088
7.0	4.412698	779	779
8.0	4.709207	539	539
9.0	4.958445	434	434
10.0	5.167949	364	364
11.0	5.344053	301	301
12.0	5.492081	253	253
13.0	5.616511	204	204
14.0	5.721103	189	189
15.0	5.809021	178	178
16.0	5.882922	152	152
17.0	5.945042	163	163
18.0	5.997258	137	137
19.0	6.04115	132	132
20.0	6.078045	129	129
21.0	6.109057	100	100
22.0	6.135125	112	112
23.0	6.157038	108	108
24.0	6.175457	87	87
25.0	6.19094	99	99
26.0	6.203954	88	88
27.0	6.214894	58	58
28.0	6.224089	60	60
29.0	6.231819	50	50
30.0	6.238316	42	42
31.0	6.243777	63	63
32.0	6.248368	47	47
33.0	6.252227	39	39
34.0	6.255471	38	38
35.0	6.258197	28	28
36.0	6.260489	34	34
37.0	6.262415	35	35
38.0	6.264035	30	30
39.0	6.265396	29	29
40.0	6.26654	19	19
41.0	6.267502	29	29
42.0	6.26831	33	33
43.0	6.26899	29	29
44.0	6.269561	26	26
45.0	6.270041	23	23
46.0	6.270445	17	17
47.0	6.270784	19	19
48.0	6.271069	16	16
49.0	6.271309	20	20
50.0	6.271511	19	19
51.0	6.27168	18	18
52.0	6.271822	19	19
53.0	6.271942	22	22
54.0	6.272043	15	15
55.0	6.272127	13	13
56.0	6.272198	23	23
57.0	6.272258	19	19
58.0	6.272308	14	14
59.0	6.27235	15	15
60.0	6.272386	16	16
61.0	6.272416	12	12
62.0	6.272441	19	19
63.0	6.272462	16	16
64.0	6.27248	18	18
65.0	6.272495	12	12
66.0	6.272507	11	11
67.0	6.272518	11	11
68.0	6.272526	16	16
69.0	6.272534	8	8
70.0	6.27254	11	11
71.0	6.272545	14	14
72.0	6.27255	12	12
73.0	6.272553	8	8
74.0	6.272557	9	9
75.0	6.272559	11	11
76.0	6.272561	12	12
77.0	6.272563	6	6
78.0	6.272565	8	8
79.0	6.272566	14	14
80.0	6.272567	9	9
81.0	6.272568	8	8
82.0	6.272569	5	5
83.0	6.27257	10	10
84.0	6.27257	6	6
85.0	6.272571	6	6
86.0	6.272571	14	14
87.0	6.272571	10	10
88.0	6.272572	6	6
89.0	6.272572	2	2
90.0	6.272572	6	6
91.0	6.272572	7	7
92.0	6.272572	11	11
93.0	6.272572	11	11
94.0	6.272573	8	8
95.0	6.272573	7	7
96.0	6.272573	4	4
97.0	6.272573	3	3
98.0	6.272573	9	9
99.0	6.272573	1	1
100.0	6.272573	4	4
101.0	0	4	4
102.0	0	6	6
103.0	0	4	4
104.0	0	4	4
105.0	0	3	3
106.0	0	7	7
107.0	0	4	4
108.0	0	1	1
109.0	0	3	3
110.0	0	4	4
111.0	0	1	1
112.0	0	3	3
113.0	0	2	2
114.0	0	1	1
115.0	0	1	1
116.0	0	4	4
117.0	0	3	3
118.0	0	1	1
119.0	0	4	4
120.0	0	1	1
121.0	0	3	3
122.0	0	4	4
123.0	0	3	3
125.0	0	3	3
126.0	0	1	1
127.0	0	3	3
128.0	0	3	3
129.0	0	4	4
130.0	0	3	3
131.0	0	2	2
132.0	0	3	3
133.0	0	3	3
134.0	0	4	4
135.0	0	1	1
136.0	0	1	1
137.0	0	3	3
138.0	0	3	3
139.0	0	3	3
142.0	0	3	3
143.0	0	5	5
144.0	0	4	4
145.0	0	1	1
148.0	0	1	1
150.0	0	1	1
151.0	0	1	1
153.0	0	1	1
154.0	0	1	1
155.0	0	3	3
157.0	0	2	2
158.0	0	3	3
159.0	0	2	2
162.0	0	1	1
163.0	0	1	1
164.0	0	2	2
166.0	0	1	1
167.0	0	2	2
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
173.0	0	2	2
174.0	0	1	1
176.0	0	2	2
180.0	0	4	4
181.0	0	1	1
182.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
189.0	0	1	1
201.0	0	3	3
204.0	0	2	2
207.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	3	3
217.0	0	2	2
219.0	0	1	1
220.0	0	2	2
222.0	0	1	1
225.0	0	1	1
227.0	0	2	2
229.0	0	1	1
233.0	0	1	1
234.0	0	1	1
237.0	0	1	1
240.0	0	1	1
242.0	0	1	1
243.0	0	1	1
245.0	0	1	1
248.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	3	3
264.0	0	1	1
269.0	0	2	2
296.0	0	1	1
306.0	0	1	1
307.0	0	2	2
308.0	0	1	1
309.0	0	1	1
310.0	0	1	1
312.0	0	1	1
315.0	0	1	1
316.0	0	1	1
326.0	0	1	1
335.0	0	1	1
344.0	0	1	1
348.0	0	1	1
349.0	0	1	1
372.0	0	1	1
407.0	0	1	1
416.0	0	1	1
461.0	0	1	1
464.0	0	1	1
478.0	0	1	1
542.0	0	1	1
564.0	0	2	2
680.0	0	1	1
684.0	0	1	1
1035.0	0	1	1
1983.0	0	1	1