## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-04/UA_Kie_Cho_1_2016-09-04.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-04/UA_Kie_Cho_1_2016-09-04.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-04/UA_Kie_Cho_1_2016-09-04.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 09:05:13 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	30587056	12381538	0	0	7463244	1063317	0	0.173258	67897790

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10226531	10226531
2.0	1.833305	720346	720346
3.0	2.527702	58500	58500
4.0	3.106347	6876	6876
5.0	3.588535	2044	2044
6.0	3.990344	1161	1161
7.0	4.325174	836	836
8.0	4.604189	606	606
9.0	4.836694	484	484
10.0	5.030441	379	379
11.0	5.191892	283	283
12.0	5.326429	253	253
13.0	5.43854	198	198
14.0	5.531963	202	202
15.0	5.609812	157	157
16.0	5.674685	145	145
17.0	5.728743	142	142
18.0	5.773791	123	123
19.0	5.811329	101	101
20.0	5.842609	122	122
21.0	5.868676	105	105
22.0	5.890397	98	98
23.0	5.908497	93	93
24.0	5.92358	84	84
25.0	5.936149	83	83
26.0	5.946623	80	80
27.0	5.955351	94	94
28.0	5.962624	72	72
29.0	5.968684	54	54
30.0	5.973734	58	58
31.0	5.977943	62	62
32.0	5.98145	47	47
33.0	5.984372	59	59
34.0	5.986807	42	42
35.0	5.988837	38	38
36.0	5.990528	35	35
37.0	5.991937	42	42
38.0	5.993111	39	39
39.0	5.994089	45	45
40.0	5.994905	32	32
41.0	5.995584	27	27
42.0	5.99615	35	35
43.0	5.996622	34	34
44.0	5.997015	25	25
45.0	5.997343	25	25
46.0	5.997616	27	27
47.0	5.997843	25	25
48.0	5.998033	27	27
49.0	5.998191	18	18
50.0	5.998323	24	24
51.0	5.998432	18	18
52.0	5.998524	15	15
53.0	5.9986	17	17
54.0	5.998663	22	22
55.0	5.998716	12	12
56.0	5.99876	19	19
57.0	5.998797	18	18
58.0	5.998828	12	12
59.0	5.998853	13	13
60.0	5.998875	17	17
61.0	5.998892	19	19
62.0	5.998907	8	8
63.0	5.998919	14	14
64.0	5.99893	9	9
65.0	5.998938	9	9
66.0	5.998945	4	4
67.0	5.998951	14	14
68.0	5.998956	20	20
69.0	5.99896	7	7
70.0	5.998964	12	12
71.0	5.998966	11	11
72.0	5.998969	13	13
73.0	5.998971	14	14
74.0	5.998972	20	20
75.0	5.998974	9	9
76.0	5.998975	12	12
77.0	5.998976	8	8
78.0	5.998977	8	8
79.0	5.998977	7	7
80.0	5.998978	12	12
81.0	5.998978	9	9
82.0	5.998979	10	10
83.0	5.998979	8	8
84.0	5.998979	4	4
85.0	5.99898	14	14
86.0	5.99898	13	13
87.0	5.99898	10	10
88.0	5.99898	7	7
89.0	5.99898	13	13
90.0	5.99898	9	9
91.0	5.99898	18	18
92.0	5.99898	5	5
93.0	5.99898	6	6
94.0	5.998981	11	11
95.0	5.998981	11	11
96.0	5.998981	7	7
97.0	5.998981	7	7
98.0	5.998981	3	3
99.0	5.998981	6	6
100.0	5.998981	7	7
101.0	0	8	8
102.0	0	4	4
103.0	0	14	14
104.0	0	5	5
105.0	0	1	1
106.0	0	5	5
107.0	0	8	8
108.0	0	4	4
109.0	0	8	8
110.0	0	9	9
111.0	0	7	7
112.0	0	3	3
113.0	0	1	1
114.0	0	4	4
115.0	0	12	12
116.0	0	8	8
117.0	0	4	4
118.0	0	5	5
119.0	0	2	2
120.0	0	4	4
122.0	0	3	3
123.0	0	6	6
124.0	0	2	2
125.0	0	3	3
126.0	0	2	2
127.0	0	3	3
128.0	0	3	3
129.0	0	2	2
130.0	0	1	1
131.0	0	3	3
132.0	0	7	7
133.0	0	2	2
134.0	0	1	1
135.0	0	3	3
136.0	0	5	5
137.0	0	5	5
138.0	0	2	2
139.0	0	3	3
140.0	0	5	5
141.0	0	2	2
142.0	0	6	6
143.0	0	1	1
144.0	0	1	1
145.0	0	1	1
146.0	0	4	4
147.0	0	5	5
148.0	0	1	1
149.0	0	1	1
150.0	0	2	2
151.0	0	5	5
152.0	0	3	3
153.0	0	2	2
156.0	0	1	1
157.0	0	2	2
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
163.0	0	3	3
164.0	0	2	2
165.0	0	1	1
172.0	0	1	1
174.0	0	1	1
177.0	0	1	1
179.0	0	2	2
180.0	0	2	2
182.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
188.0	0	3	3
191.0	0	2	2
192.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	1	1
197.0	0	2	2
198.0	0	3	3
199.0	0	1	1
200.0	0	1	1
201.0	0	2	2
202.0	0	2	2
204.0	0	1	1
206.0	0	1	1
211.0	0	2	2
212.0	0	1	1
213.0	0	4	4
214.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	2	2
219.0	0	1	1
220.0	0	1	1
222.0	0	2	2
224.0	0	1	1
230.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	1	1
239.0	0	1	1
244.0	0	1	1
254.0	0	1	1
256.0	0	1	1
259.0	0	1	1
262.0	0	1	1
265.0	0	1	1
269.0	0	1	1
271.0	0	1	1
274.0	0	2	2
275.0	0	2	2
284.0	0	1	1
286.0	0	1	1
287.0	0	1	1
290.0	0	1	1
296.0	0	1	1
305.0	0	1	1
307.0	0	1	1
310.0	0	2	2
311.0	0	2	2
315.0	0	1	1
321.0	0	2	2
323.0	0	1	1
325.0	0	1	1
338.0	0	3	3
348.0	0	1	1
349.0	0	1	1
361.0	0	1	1
362.0	0	1	1
366.0	0	1	1
373.0	0	1	1
379.0	0	1	1
390.0	0	2	2
402.0	0	1	1
403.0	0	1	1
406.0	0	1	1
407.0	0	2	2
415.0	0	1	1
419.0	0	1	1
434.0	0	1	1
438.0	0	1	1
464.0	0	1	1
508.0	0	1	1
519.0	0	1	1
539.0	0	1	1
601.0	0	1	1
685.0	0	1	1
743.0	0	1	1
766.0	0	1	1
870.0	0	1	1
1168.0	0	1	1
2006.0	0	1	1