## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2013-09-22/US_Wis_Cro_1_2013-09-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2013-09-22/US_Wis_Cro_1_2013-09-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2013-09-22/US_Wis_Cro_1_2013-09-22.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 21:02:17 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	853341	51326265	0	0	417991	23745321	0	0.462859	36563699

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	12897367	12897367
2.0	1.245674	7562844	7562844
3.0	1.30603	3706572	3706572
4.0	1.320858	1553519	1553519
5.0	1.324501	580574	580574
6.0	1.325396	197464	197464
7.0	1.325615	64502	64502
8.0	1.325669	20741	20741
9.0	1.325683	7329	7329
10.0	1.325686	2912	2912
11.0	1.325687	1441	1441
12.0	1.325687	869	869
13.0	1.325687	615	615
14.0	1.325687	414	414
15.0	1.325687	362	362
16.0	1.325687	278	278
17.0	1.325687	224	224
18.0	1.325687	179	179
19.0	1.325687	164	164
20.0	1.325687	164	164
21.0	1.325687	121	121
22.0	1.325687	99	99
23.0	1.325687	88	88
24.0	1.325687	80	80
25.0	1.325687	66	66
26.0	1.325687	82	82
27.0	1.325687	52	52
28.0	1.325687	52	52
29.0	1.325687	59	59
30.0	1.325687	35	35
31.0	1.325687	53	53
32.0	1.325687	42	42
33.0	1.325687	31	31
34.0	1.325687	37	37
35.0	1.325687	47	47
36.0	1.325687	23	23
37.0	1.325687	37	37
38.0	1.325687	33	33
39.0	1.325687	26	26
40.0	1.325687	33	33
41.0	1.325687	18	18
42.0	1.325687	27	27
43.0	1.325687	17	17
44.0	1.325687	17	17
45.0	1.325687	17	17
46.0	1.325687	23	23
47.0	1.325687	14	14
48.0	1.325687	14	14
49.0	1.325687	16	16
50.0	1.325687	14	14
51.0	1.325687	16	16
52.0	1.325687	19	19
53.0	1.325687	14	14
54.0	1.325687	11	11
55.0	1.325687	11	11
56.0	1.325687	5	5
57.0	1.325687	21	21
58.0	1.325687	13	13
59.0	1.325687	11	11
60.0	1.325687	15	15
61.0	1.325687	13	13
62.0	1.325687	7	7
63.0	1.325687	11	11
64.0	1.325687	9	9
65.0	1.325687	7	7
66.0	1.325687	10	10
67.0	1.325687	10	10
68.0	1.325687	10	10
69.0	1.325687	11	11
70.0	1.325687	6	6
71.0	1.325687	7	7
72.0	1.325687	8	8
73.0	1.325687	3	3
74.0	1.325687	7	7
75.0	1.325687	4	4
76.0	1.325687	7	7
77.0	1.325687	3	3
78.0	1.325687	4	4
79.0	1.325687	5	5
80.0	1.325687	6	6
81.0	1.325687	4	4
82.0	1.325687	3	3
83.0	1.325687	6	6
84.0	1.325687	4	4
85.0	1.325687	6	6
86.0	1.325687	9	9
87.0	1.325687	2	2
88.0	1.325687	4	4
89.0	1.325687	4	4
90.0	1.325687	3	3
91.0	1.325687	7	7
92.0	1.325687	2	2
93.0	1.325687	3	3
94.0	1.325687	5	5
95.0	1.325687	4	4
96.0	1.325687	4	4
97.0	1.325687	3	3
98.0	1.325687	2	2
99.0	1.325687	1	1
100.0	1.325687	2	2
101.0	0	3	3
102.0	0	3	3
103.0	0	10	10
104.0	0	5	5
105.0	0	5	5
106.0	0	5	5
107.0	0	2	2
108.0	0	2	2
109.0	0	1	1
110.0	0	3	3
111.0	0	1	1
112.0	0	2	2
113.0	0	3	3
114.0	0	2	2
115.0	0	3	3
116.0	0	5	5
117.0	0	2	2
118.0	0	2	2
119.0	0	1	1
120.0	0	2	2
121.0	0	3	3
122.0	0	7	7
123.0	0	2	2
125.0	0	3	3
126.0	0	1	1
127.0	0	2	2
128.0	0	3	3
129.0	0	3	3
130.0	0	2	2
131.0	0	1	1
132.0	0	5	5
133.0	0	1	1
135.0	0	1	1
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
141.0	0	3	3
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
146.0	0	1	1
147.0	0	2	2
149.0	0	1	1
151.0	0	2	2
152.0	0	3	3
153.0	0	1	1
154.0	0	2	2
156.0	0	1	1
158.0	0	1	1
159.0	0	1	1
161.0	0	2	2
162.0	0	1	1
163.0	0	1	1
165.0	0	2	2
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	3	3
174.0	0	2	2
175.0	0	1	1
177.0	0	1	1
183.0	0	1	1
185.0	0	1	1
186.0	0	1	1
190.0	0	1	1
192.0	0	2	2
194.0	0	4	4
196.0	0	1	1
197.0	0	3	3
198.0	0	3	3
200.0	0	2	2
201.0	0	1	1
203.0	0	1	1
207.0	0	1	1
209.0	0	1	1
211.0	0	2	2
212.0	0	1	1
214.0	0	1	1
215.0	0	1	1
217.0	0	2	2
221.0	0	1	1
223.0	0	1	1
224.0	0	2	2
226.0	0	1	1
227.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
234.0	0	1	1
236.0	0	3	3
237.0	0	1	1
238.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
244.0	0	2	2
245.0	0	1	1
246.0	0	1	1
251.0	0	1	1
257.0	0	1	1
258.0	0	1	1
264.0	0	1	1
269.0	0	5	5
273.0	0	1	1
275.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	1	1
285.0	0	1	1
291.0	0	1	1
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
308.0	0	1	1
311.0	0	1	1
314.0	0	2	2
315.0	0	1	1
316.0	0	1	1
320.0	0	1	1
334.0	0	1	1
337.0	0	1	1
340.0	0	1	1
345.0	0	1	1
351.0	0	2	2
356.0	0	1	1
357.0	0	1	1
371.0	0	1	1
391.0	0	1	1
392.0	0	1	1
395.0	0	1	1
413.0	0	1	1
425.0	0	1	1
426.0	0	1	1
428.0	0	1	1
432.0	0	1	1
433.0	0	1	1
436.0	0	1	1
438.0	0	1	1
445.0	0	1	1
453.0	0	1	1
460.0	0	1	1
463.0	0	1	1
474.0	0	1	1
487.0	0	1	1
495.0	0	1	1
502.0	0	1	1
526.0	0	1	1
529.0	0	1	1
554.0	0	1	1
594.0	0	1	1
637.0	0	1	1
688.0	0	1	1
695.0	0	1	1
743.0	0	1	1
812.0	0	1	1
876.0	0	1	1
1010.0	0	1	1
1132.0	0	1	1
1229.0	0	1	1
1297.0	0	1	1
1681.0	0	1	1