## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2016-08-26/UA_Che_Var_1_2016-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2016-08-26/UA_Che_Var_1_2016-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2016-08-26/UA_Che_Var_1_2016-08-26.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 08:45:47 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	30179190	7803192	0	0	7066233	692538	0	0.184585	41319871

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	6426590	6426590
2.0	1.827912	386809	386809
3.0	2.51335	30483	30483
4.0	3.080833	4428	4428
5.0	3.550658	1828	1828
6.0	3.939633	1100	1100
7.0	4.261669	834	834
8.0	4.528287	558	558
9.0	4.749023	422	422
10.0	4.931773	341	341
11.0	5.083074	311	311
12.0	5.208338	257	257
13.0	5.312046	200	200
14.0	5.397906	176	176
15.0	5.468991	168	168
16.0	5.527844	174	174
17.0	5.576568	119	119
18.0	5.616908	154	154
19.0	5.650305	124	124
20.0	5.677955	115	115
21.0	5.700847	113	113
22.0	5.7198	106	106
23.0	5.735491	94	94
24.0	5.748482	95	95
25.0	5.759237	87	87
26.0	5.768142	77	77
27.0	5.775514	73	73
28.0	5.781617	67	67
29.0	5.78667	72	72
30.0	5.790854	52	52
31.0	5.794317	56	56
32.0	5.797185	49	49
33.0	5.799559	64	64
34.0	5.801524	57	57
35.0	5.803152	47	47
36.0	5.804499	49	49
37.0	5.805614	49	49
38.0	5.806538	33	33
39.0	5.807302	35	35
40.0	5.807935	34	34
41.0	5.808459	28	28
42.0	5.808893	32	32
43.0	5.809252	30	30
44.0	5.80955	22	22
45.0	5.809796	24	24
46.0	5.81	25	25
47.0	5.810168	20	20
48.0	5.810308	28	28
49.0	5.810424	27	27
50.0	5.81052	27	27
51.0	5.810599	22	22
52.0	5.810665	16	16
53.0	5.810719	16	16
54.0	5.810764	14	14
55.0	5.810801	14	14
56.0	5.810832	19	19
57.0	5.810858	15	15
58.0	5.810879	16	16
59.0	5.810896	7	7
60.0	5.810911	19	19
61.0	5.810923	15	15
62.0	5.810933	9	9
63.0	5.810941	12	12
64.0	5.810948	18	18
65.0	5.810953	18	18
66.0	5.810958	15	15
67.0	5.810962	9	9
68.0	5.810965	10	10
69.0	5.810968	21	21
70.0	5.81097	9	9
71.0	5.810972	12	12
72.0	5.810973	15	15
73.0	5.810974	7	7
74.0	5.810975	11	11
75.0	5.810976	5	5
76.0	5.810977	9	9
77.0	5.810978	8	8
78.0	5.810978	7	7
79.0	5.810978	13	13
80.0	5.810979	14	14
81.0	5.810979	9	9
82.0	5.810979	11	11
83.0	5.810979	12	12
84.0	5.81098	9	9
85.0	5.81098	7	7
86.0	5.81098	8	8
87.0	5.81098	6	6
88.0	5.81098	10	10
89.0	5.81098	7	7
90.0	5.81098	12	12
91.0	5.81098	5	5
92.0	5.81098	10	10
93.0	5.81098	3	3
94.0	5.81098	6	6
95.0	5.81098	3	3
96.0	5.81098	10	10
97.0	5.81098	9	9
98.0	5.81098	8	8
99.0	5.81098	1	1
100.0	5.81098	7	7
101.0	0	10	10
102.0	0	2	2
103.0	0	6	6
104.0	0	7	7
105.0	0	9	9
106.0	0	9	9
107.0	0	4	4
108.0	0	4	4
109.0	0	6	6
110.0	0	4	4
111.0	0	3	3
112.0	0	3	3
113.0	0	2	2
114.0	0	5	5
115.0	0	4	4
116.0	0	4	4
117.0	0	6	6
118.0	0	5	5
119.0	0	4	4
120.0	0	5	5
121.0	0	3	3
122.0	0	4	4
123.0	0	3	3
124.0	0	4	4
125.0	0	8	8
126.0	0	3	3
127.0	0	1	1
128.0	0	5	5
129.0	0	4	4
130.0	0	1	1
131.0	0	3	3
132.0	0	3	3
133.0	0	5	5
134.0	0	2	2
135.0	0	3	3
136.0	0	2	2
137.0	0	2	2
138.0	0	3	3
139.0	0	5	5
140.0	0	5	5
141.0	0	2	2
142.0	0	1	1
143.0	0	5	5
144.0	0	4	4
145.0	0	8	8
146.0	0	3	3
147.0	0	4	4
149.0	0	3	3
150.0	0	3	3
151.0	0	2	2
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
155.0	0	3	3
156.0	0	2	2
157.0	0	2	2
159.0	0	2	2
160.0	0	2	2
163.0	0	2	2
164.0	0	3	3
166.0	0	2	2
168.0	0	1	1
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	2	2
174.0	0	4	4
175.0	0	3	3
177.0	0	1	1
179.0	0	1	1
180.0	0	2	2
182.0	0	1	1
183.0	0	1	1
185.0	0	2	2
186.0	0	1	1
187.0	0	1	1
188.0	0	2	2
189.0	0	2	2
190.0	0	1	1
191.0	0	3	3
193.0	0	1	1
195.0	0	2	2
196.0	0	1	1
199.0	0	2	2
201.0	0	2	2
204.0	0	1	1
209.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
215.0	0	2	2
217.0	0	1	1
219.0	0	1	1
222.0	0	1	1
224.0	0	1	1
225.0	0	2	2
226.0	0	1	1
228.0	0	2	2
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
233.0	0	2	2
235.0	0	1	1
236.0	0	3	3
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	2	2
242.0	0	1	1
243.0	0	2	2
244.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
250.0	0	3	3
253.0	0	1	1
255.0	0	1	1
257.0	0	1	1
258.0	0	2	2
261.0	0	2	2
265.0	0	1	1
269.0	0	1	1
271.0	0	1	1
275.0	0	2	2
276.0	0	1	1
279.0	0	1	1
282.0	0	2	2
285.0	0	1	1
287.0	0	1	1
290.0	0	2	2
291.0	0	1	1
292.0	0	1	1
294.0	0	1	1
295.0	0	2	2
299.0	0	1	1
300.0	0	1	1
301.0	0	2	2
304.0	0	1	1
305.0	0	2	2
309.0	0	1	1
310.0	0	1	1
315.0	0	1	1
319.0	0	1	1
320.0	0	1	1
325.0	0	1	1
327.0	0	2	2
331.0	0	1	1
334.0	0	1	1
335.0	0	1	1
336.0	0	1	1
338.0	0	1	1
341.0	0	1	1
345.0	0	1	1
346.0	0	1	1
350.0	0	1	1
353.0	0	1	1
354.0	0	1	1
359.0	0	1	1
363.0	0	1	1
366.0	0	1	1
374.0	0	1	1
377.0	0	2	2
378.0	0	2	2
380.0	0	1	1
381.0	0	1	1
403.0	0	2	2
412.0	0	1	1
415.0	0	1	1
425.0	0	1	1
450.0	0	1	1
455.0	0	1	1
459.0	0	1	1
460.0	0	1	1
480.0	0	1	1
488.0	0	1	1
508.0	0	1	1
528.0	0	1	1
576.0	0	1	1
643.0	0	1	1
685.0	0	1	1
695.0	0	1	1
701.0	0	1	1
713.0	0	1	1
716.0	0	1	1
814.0	0	1	1
844.0	0	1	1
869.0	0	1	1
883.0	0	1	1
944.0	0	1	1
965.0	0	1	1
1231.0	0	1	1
1277.0	0	1	1
1325.0	0	1	1
1470.0	0	1	1
2354.0	0	1	1
4548.0	0	1	1