## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Kan_1_2016-07-08/UA_Che_Kan_1_2016-07-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Kan_1_2016-07-08/UA_Che_Kan_1_2016-07-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Kan_1_2016-07-08/UA_Che_Kan_1_2016-07-08.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 09:03:54 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	32966929	12118795	0	0	8240283	1011203	0	0.179403	68520620

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10079678	10079678
2.0	1.837894	654165	654165
3.0	2.539961	49445	49445
4.0	3.128218	6097	6097
5.0	3.621116	2127	2127
6.0	4.034112	1226	1226
7.0	4.380159	882	882
8.0	4.67011	618	618
9.0	4.913058	478	478
10.0	5.116622	381	381
11.0	5.287188	290	290
12.0	5.430104	227	227
13.0	5.549852	238	238
14.0	5.650189	168	168
15.0	5.73426	139	139
16.0	5.804703	149	149
17.0	5.863727	118	118
18.0	5.913183	139	139
19.0	5.954621	104	104
20.0	5.989343	122	122
21.0	6.018435	105	105
22.0	6.042812	82	82
23.0	6.063237	94	94
24.0	6.080351	115	115
25.0	6.09469	69	69
26.0	6.106706	96	96
27.0	6.116773	92	92
28.0	6.125208	66	66
29.0	6.132276	60	60
30.0	6.138199	74	74
31.0	6.143161	58	58
32.0	6.147319	62	62
33.0	6.150802	65	65
34.0	6.153722	55	55
35.0	6.156167	47	47
36.0	6.158217	44	44
37.0	6.159934	50	50
38.0	6.161373	37	37
39.0	6.162578	45	45
40.0	6.163588	44	44
41.0	6.164435	35	35
42.0	6.165144	35	35
43.0	6.165738	33	33
44.0	6.166236	23	23
45.0	6.166653	35	35
46.0	6.167003	15	15
47.0	6.167296	25	25
48.0	6.167541	31	31
49.0	6.167747	16	16
50.0	6.167919	31	31
51.0	6.168063	18	18
52.0	6.168184	22	22
53.0	6.168286	20	20
54.0	6.168371	18	18
55.0	6.168442	17	17
56.0	6.168501	22	22
57.0	6.168551	18	18
58.0	6.168593	13	13
59.0	6.168628	15	15
60.0	6.168658	16	16
61.0	6.168682	11	11
62.0	6.168703	15	15
63.0	6.16872	9	9
64.0	6.168735	11	11
65.0	6.168747	8	8
66.0	6.168757	9	9
67.0	6.168766	17	17
68.0	6.168773	12	12
69.0	6.168779	9	9
70.0	6.168784	10	10
71.0	6.168788	10	10
72.0	6.168791	12	12
73.0	6.168794	9	9
74.0	6.168797	10	10
75.0	6.168799	13	13
76.0	6.168801	8	8
77.0	6.168802	15	15
78.0	6.168803	15	15
79.0	6.168804	10	10
80.0	6.168805	11	11
81.0	6.168806	6	6
82.0	6.168806	8	8
83.0	6.168807	11	11
84.0	6.168807	10	10
85.0	6.168808	13	13
86.0	6.168808	13	13
87.0	6.168808	9	9
88.0	6.168809	9	9
89.0	6.168809	7	7
90.0	6.168809	14	14
91.0	6.168809	9	9
92.0	6.168809	16	16
93.0	6.168809	12	12
94.0	6.168809	14	14
95.0	6.168809	7	7
96.0	6.168809	9	9
97.0	6.168809	3	3
98.0	6.168809	7	7
99.0	6.168809	5	5
100.0	6.168809	10	10
101.0	0	10	10
102.0	0	5	5
103.0	0	4	4
104.0	0	5	5
105.0	0	5	5
106.0	0	10	10
107.0	0	7	7
108.0	0	6	6
109.0	0	9	9
110.0	0	7	7
111.0	0	5	5
112.0	0	12	12
113.0	0	7	7
114.0	0	5	5
115.0	0	5	5
116.0	0	3	3
117.0	0	3	3
118.0	0	5	5
119.0	0	6	6
120.0	0	5	5
121.0	0	2	2
122.0	0	3	3
123.0	0	6	6
124.0	0	1	1
125.0	0	7	7
126.0	0	1	1
127.0	0	4	4
128.0	0	4	4
129.0	0	4	4
130.0	0	3	3
131.0	0	9	9
132.0	0	3	3
133.0	0	5	5
134.0	0	7	7
135.0	0	3	3
136.0	0	4	4
137.0	0	2	2
138.0	0	7	7
139.0	0	4	4
140.0	0	1	1
141.0	0	3	3
142.0	0	1	1
143.0	0	6	6
144.0	0	5	5
145.0	0	4	4
146.0	0	4	4
147.0	0	3	3
148.0	0	3	3
149.0	0	4	4
150.0	0	7	7
151.0	0	5	5
153.0	0	5	5
154.0	0	3	3
156.0	0	1	1
159.0	0	3	3
160.0	0	1	1
161.0	0	2	2
162.0	0	1	1
163.0	0	2	2
166.0	0	2	2
167.0	0	1	1
168.0	0	2	2
169.0	0	2	2
172.0	0	2	2
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
177.0	0	3	3
178.0	0	1	1
179.0	0	2	2
180.0	0	2	2
181.0	0	2	2
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
188.0	0	3	3
189.0	0	2	2
190.0	0	1	1
191.0	0	1	1
192.0	0	2	2
193.0	0	3	3
194.0	0	3	3
195.0	0	2	2
196.0	0	3	3
199.0	0	2	2
201.0	0	2	2
202.0	0	3	3
203.0	0	1	1
204.0	0	1	1
206.0	0	4	4
207.0	0	2	2
208.0	0	1	1
210.0	0	2	2
211.0	0	2	2
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
220.0	0	1	1
221.0	0	2	2
222.0	0	1	1
224.0	0	1	1
225.0	0	2	2
232.0	0	1	1
238.0	0	1	1
240.0	0	2	2
242.0	0	1	1
243.0	0	1	1
246.0	0	1	1
247.0	0	2	2
248.0	0	2	2
250.0	0	1	1
251.0	0	1	1
253.0	0	2	2
254.0	0	1	1
258.0	0	1	1
262.0	0	2	2
263.0	0	1	1
264.0	0	1	1
266.0	0	2	2
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
276.0	0	2	2
278.0	0	1	1
279.0	0	2	2
280.0	0	1	1
289.0	0	2	2
293.0	0	1	1
296.0	0	1	1
311.0	0	1	1
312.0	0	2	2
313.0	0	1	1
317.0	0	1	1
319.0	0	1	1
333.0	0	1	1
337.0	0	1	1
338.0	0	1	1
342.0	0	1	1
345.0	0	1	1
346.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	1	1
360.0	0	1	1
365.0	0	3	3
368.0	0	1	1
369.0	0	1	1
376.0	0	1	1
379.0	0	1	1
381.0	0	2	2
385.0	0	1	1
388.0	0	1	1
391.0	0	3	3
394.0	0	1	1
400.0	0	1	1
404.0	0	1	1
407.0	0	1	1
412.0	0	1	1
415.0	0	1	1
423.0	0	1	1
431.0	0	2	2
433.0	0	1	1
444.0	0	1	1
451.0	0	1	1
455.0	0	1	1
472.0	0	1	1
474.0	0	1	1
491.0	0	1	1
492.0	0	1	1
494.0	0	1	1
498.0	0	1	1
570.0	0	1	1
578.0	0	1	1
592.0	0	1	1
602.0	0	1	1
609.0	0	1	1
621.0	0	1	1
688.0	0	1	1
721.0	0	1	1
800.0	0	1	1
861.0	0	1	1
929.0	0	1	1
1035.0	0	1	1
1148.0	0	1	1
1152.0	0	1	1
1729.0	0	1	1
3611.0	0	1	1