## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2016-07-29/FI_Cen_Ves_1_2016-07-29.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2016-07-29/FI_Cen_Ves_1_2016-07-29.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2016-07-29/FI_Cen_Ves_1_2016-07-29.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 09:14:11 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	38429494	12926226	0	0	10216592	1041905	0	0.191351	75814310

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10812988	10812988
2.0	1.843244	705346	705346
3.0	2.554305	53413	53413
4.0	3.153904	6031	6031
5.0	3.659511	1723	1723
6.0	4.085862	1060	1060
7.0	4.44538	689	689
8.0	4.748542	502	502
9.0	5.004181	344	344
10.0	5.219748	293	293
11.0	5.401523	234	234
12.0	5.554803	217	217
13.0	5.684057	159	159
14.0	5.793049	158	158
15.0	5.884956	120	120
16.0	5.962456	111	111
17.0	6.027807	98	98
18.0	6.082914	93	93
19.0	6.129383	110	110
20.0	6.168568	83	83
21.0	6.20161	83	83
22.0	6.229473	65	65
23.0	6.252968	68	68
24.0	6.27278	68	68
25.0	6.289486	71	71
26.0	6.303574	69	69
27.0	6.315453	62	62
28.0	6.32547	68	68
29.0	6.333917	75	75
30.0	6.34104	50	50
31.0	6.347046	65	65
32.0	6.352111	56	56
33.0	6.356381	67	67
34.0	6.359983	59	59
35.0	6.36302	55	55
36.0	6.36558	48	48
37.0	6.36774	36	36
38.0	6.369561	49	49
39.0	6.371096	34	34
40.0	6.372391	36	36
41.0	6.373483	32	32
42.0	6.374403	34	34
43.0	6.375179	36	36
44.0	6.375834	33	33
45.0	6.376386	22	22
46.0	6.376852	31	31
47.0	6.377244	28	28
48.0	6.377575	25	25
49.0	6.377854	14	14
50.0	6.37809	20	20
51.0	6.378288	18	18
52.0	6.378455	23	23
53.0	6.378597	27	27
54.0	6.378716	30	30
55.0	6.378816	25	25
56.0	6.3789	16	16
57.0	6.378972	16	16
58.0	6.379032	13	13
59.0	6.379083	11	11
60.0	6.379125	19	19
61.0	6.379162	11	11
62.0	6.379192	15	15
63.0	6.379218	6	6
64.0	6.379239	15	15
65.0	6.379258	14	14
66.0	6.379273	15	15
67.0	6.379286	9	9
68.0	6.379297	7	7
69.0	6.379306	16	16
70.0	6.379314	7	7
71.0	6.37932	6	6
72.0	6.379326	13	13
73.0	6.379331	11	11
74.0	6.379334	13	13
75.0	6.379338	5	5
76.0	6.379341	16	16
77.0	6.379343	8	8
78.0	6.379345	8	8
79.0	6.379347	10	10
80.0	6.379348	11	11
81.0	6.379349	10	10
82.0	6.37935	9	9
83.0	6.379351	9	9
84.0	6.379352	8	8
85.0	6.379352	9	9
86.0	6.379353	6	6
87.0	6.379353	6	6
88.0	6.379354	13	13
89.0	6.379354	5	5
90.0	6.379354	14	14
91.0	6.379354	6	6
92.0	6.379355	6	6
93.0	6.379355	12	12
94.0	6.379355	8	8
95.0	6.379355	8	8
96.0	6.379355	3	3
97.0	6.379355	7	7
98.0	6.379355	3	3
99.0	6.379355	12	12
100.0	6.379355	6	6
101.0	0	10	10
102.0	0	8	8
103.0	0	6	6
104.0	0	6	6
105.0	0	6	6
106.0	0	9	9
107.0	0	6	6
108.0	0	4	4
109.0	0	8	8
110.0	0	9	9
111.0	0	14	14
112.0	0	5	5
113.0	0	6	6
114.0	0	7	7
115.0	0	6	6
116.0	0	7	7
117.0	0	9	9
118.0	0	5	5
119.0	0	2	2
120.0	0	5	5
121.0	0	6	6
122.0	0	7	7
123.0	0	1	1
124.0	0	8	8
125.0	0	4	4
126.0	0	4	4
127.0	0	5	5
128.0	0	3	3
129.0	0	2	2
130.0	0	4	4
131.0	0	5	5
132.0	0	9	9
133.0	0	3	3
134.0	0	6	6
135.0	0	1	1
136.0	0	3	3
137.0	0	4	4
138.0	0	2	2
139.0	0	10	10
140.0	0	2	2
141.0	0	6	6
142.0	0	3	3
143.0	0	4	4
144.0	0	2	2
145.0	0	4	4
146.0	0	3	3
147.0	0	1	1
149.0	0	2	2
150.0	0	4	4
151.0	0	2	2
152.0	0	3	3
153.0	0	2	2
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
159.0	0	3	3
160.0	0	1	1
161.0	0	1	1
163.0	0	3	3
164.0	0	2	2
165.0	0	1	1
167.0	0	2	2
168.0	0	2	2
170.0	0	2	2
171.0	0	2	2
172.0	0	3	3
173.0	0	1	1
174.0	0	3	3
175.0	0	1	1
176.0	0	2	2
177.0	0	3	3
179.0	0	1	1
181.0	0	2	2
182.0	0	1	1
183.0	0	3	3
184.0	0	2	2
185.0	0	1	1
186.0	0	3	3
188.0	0	1	1
189.0	0	2	2
190.0	0	1	1
191.0	0	3	3
194.0	0	1	1
195.0	0	3	3
196.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	1	1
205.0	0	1	1
207.0	0	2	2
211.0	0	2	2
212.0	0	5	5
213.0	0	3	3
214.0	0	1	1
218.0	0	4	4
219.0	0	1	1
221.0	0	1	1
228.0	0	1	1
232.0	0	1	1
235.0	0	1	1
236.0	0	2	2
238.0	0	2	2
240.0	0	1	1
241.0	0	1	1
242.0	0	2	2
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
251.0	0	1	1
252.0	0	1	1
257.0	0	1	1
262.0	0	2	2
271.0	0	1	1
272.0	0	1	1
273.0	0	2	2
274.0	0	1	1
278.0	0	1	1
280.0	0	1	1
284.0	0	1	1
288.0	0	2	2
291.0	0	2	2
301.0	0	1	1
312.0	0	1	1
315.0	0	1	1
319.0	0	1	1
320.0	0	1	1
322.0	0	1	1
324.0	0	2	2
325.0	0	1	1
330.0	0	1	1
334.0	0	1	1
337.0	0	1	1
341.0	0	1	1
349.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	1	1
356.0	0	1	1
359.0	0	1	1
360.0	0	1	1
367.0	0	1	1
378.0	0	1	1
379.0	0	1	1
383.0	0	1	1
393.0	0	1	1
396.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
413.0	0	1	1
418.0	0	1	1
419.0	0	3	3
425.0	0	1	1
426.0	0	1	1
435.0	0	1	1
442.0	0	1	1
457.0	0	2	2
472.0	0	1	1
485.0	0	1	1
490.0	0	1	1
498.0	0	1	1
499.0	0	1	1
518.0	0	1	1
524.0	0	1	1
526.0	0	2	2
532.0	0	1	1
559.0	0	1	1
575.0	0	1	1
603.0	0	1	1
617.0	0	1	1
1061.0	0	1	1
2404.0	0	1	1