## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2015-08-26/UA_Kie_Cho_4_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2015-08-26/UA_Kie_Cho_4_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2015-08-26/UA_Kie_Cho_4_2015-08-26.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 16:55:14 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	8946227	32233829	0	0	4415159	8315252	0	0.286671	51193076

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17184788	17184788
2.0	1.532777	4716873	4716873
3.0	1.816629	1169157	1169157
4.0	1.967858	268591	268591
5.0	2.04843	58793	58793
6.0	2.091356	12926	12926
7.0	2.114227	3070	3070
8.0	2.126412	1038	1038
9.0	2.132903	488	488
10.0	2.136362	300	300
11.0	2.138205	246	246
12.0	2.139187	237	237
13.0	2.13971	165	165
14.0	2.139988	156	156
15.0	2.140137	144	144
16.0	2.140216	130	130
17.0	2.140258	121	121
18.0	2.14028	102	102
19.0	2.140292	106	106
20.0	2.140299	80	80
21.0	2.140302	85	85
22.0	2.140304	84	84
23.0	2.140305	79	79
24.0	2.140306	67	67
25.0	2.140306	61	61
26.0	2.140306	66	66
27.0	2.140306	58	58
28.0	2.140306	46	46
29.0	2.140306	59	59
30.0	2.140306	47	47
31.0	2.140306	42	42
32.0	2.140306	48	48
33.0	2.140306	48	48
34.0	2.140306	33	33
35.0	2.140306	37	37
36.0	2.140306	27	27
37.0	2.140306	28	28
38.0	2.140306	36	36
39.0	2.140306	32	32
40.0	2.140306	24	24
41.0	2.140306	18	18
42.0	2.140306	25	25
43.0	2.140306	30	30
44.0	2.140306	26	26
45.0	2.140306	27	27
46.0	2.140306	20	20
47.0	2.140306	15	15
48.0	2.140306	18	18
49.0	2.140306	16	16
50.0	2.140306	16	16
51.0	2.140306	18	18
52.0	2.140306	10	10
53.0	2.140306	4	4
54.0	2.140306	6	6
55.0	2.140306	13	13
56.0	2.140306	18	18
57.0	2.140306	11	11
58.0	2.140306	12	12
59.0	2.140306	10	10
60.0	2.140306	10	10
61.0	2.140306	20	20
62.0	2.140306	18	18
63.0	2.140306	8	8
64.0	2.140306	12	12
65.0	2.140306	10	10
66.0	2.140306	6	6
67.0	2.140306	9	9
68.0	2.140306	12	12
69.0	2.140306	12	12
70.0	2.140306	14	14
71.0	2.140306	9	9
72.0	2.140306	7	7
73.0	2.140306	11	11
74.0	2.140306	5	5
75.0	2.140306	7	7
76.0	2.140306	5	5
77.0	2.140306	9	9
78.0	2.140306	9	9
79.0	2.140306	9	9
80.0	2.140306	6	6
81.0	2.140306	8	8
82.0	2.140306	6	6
83.0	2.140306	10	10
84.0	2.140306	7	7
85.0	2.140306	8	8
86.0	2.140306	9	9
87.0	2.140306	4	4
88.0	2.140306	6	6
89.0	2.140306	6	6
90.0	2.140306	8	8
91.0	2.140306	7	7
92.0	2.140306	5	5
93.0	2.140306	2	2
94.0	2.140306	6	6
95.0	2.140306	5	5
96.0	2.140306	8	8
97.0	2.140306	5	5
98.0	2.140306	5	5
99.0	2.140306	3	3
100.0	2.140306	3	3
101.0	0	5	5
102.0	0	6	6
103.0	0	4	4
104.0	0	1	1
105.0	0	4	4
106.0	0	2	2
107.0	0	2	2
108.0	0	3	3
109.0	0	7	7
110.0	0	3	3
111.0	0	2	2
112.0	0	4	4
113.0	0	2	2
114.0	0	4	4
115.0	0	2	2
116.0	0	2	2
117.0	0	5	5
118.0	0	2	2
119.0	0	1	1
120.0	0	2	2
121.0	0	2	2
122.0	0	1	1
123.0	0	2	2
124.0	0	3	3
125.0	0	2	2
126.0	0	6	6
127.0	0	1	1
128.0	0	2	2
129.0	0	6	6
130.0	0	2	2
131.0	0	2	2
132.0	0	3	3
133.0	0	3	3
134.0	0	1	1
136.0	0	1	1
137.0	0	3	3
138.0	0	1	1
139.0	0	1	1
141.0	0	2	2
142.0	0	2	2
144.0	0	4	4
145.0	0	2	2
147.0	0	2	2
148.0	0	1	1
150.0	0	1	1
151.0	0	1	1
154.0	0	4	4
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
159.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
168.0	0	1	1
169.0	0	1	1
173.0	0	2	2
176.0	0	3	3
178.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	2	2
184.0	0	3	3
187.0	0	1	1
189.0	0	1	1
190.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	2	2
196.0	0	2	2
197.0	0	1	1
201.0	0	1	1
210.0	0	2	2
212.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	2	2
219.0	0	2	2
221.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
231.0	0	2	2
233.0	0	2	2
239.0	0	1	1
240.0	0	1	1
247.0	0	1	1
251.0	0	1	1
252.0	0	1	1
254.0	0	2	2
263.0	0	1	1
264.0	0	1	1
270.0	0	1	1
277.0	0	1	1
279.0	0	1	1
281.0	0	1	1
292.0	0	1	1
294.0	0	1	1
299.0	0	1	1
314.0	0	1	1
315.0	0	1	1
317.0	0	1	1
344.0	0	1	1
351.0	0	1	1
353.0	0	1	1
386.0	0	1	1
425.0	0	1	1
527.0	0	1	1
612.0	0	1	1