## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-08-06/UA_Kie_Kyi_1_2016-08-06.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-08-06/UA_Kie_Kyi_1_2016-08-06.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-08-06/UA_Kie_Kyi_1_2016-08-06.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 17:39:26 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	38651244	10560219	0	0	10830100	918593	0	0.211928	57126943

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8722386	8722386
2.0	1.831225	529604	529604
3.0	2.522159	40986	40986
4.0	3.09648	5789	5789
5.0	3.57387	2180	2180
6.0	3.970689	1400	1400
7.0	4.300534	953	953
8.0	4.574709	752	752
9.0	4.802611	517	517
10.0	4.992048	415	415
11.0	5.149513	320	320
12.0	5.280401	286	286
13.0	5.389199	234	234
14.0	5.479635	195	195
15.0	5.554807	173	173
16.0	5.617292	141	141
17.0	5.669231	150	150
18.0	5.712404	154	154
19.0	5.74829	123	123
20.0	5.77812	103	103
21.0	5.802915	116	116
22.0	5.823525	95	95
23.0	5.840657	105	105
24.0	5.854898	97	97
25.0	5.866735	83	83
26.0	5.876574	77	77
27.0	5.884752	78	78
28.0	5.891551	63	63
29.0	5.897201	67	67
30.0	5.901899	78	78
31.0	5.905803	74	74
32.0	5.909048	66	66
33.0	5.911746	51	51
34.0	5.913988	51	51
35.0	5.915852	64	64
36.0	5.917402	54	54
37.0	5.918689	49	49
38.0	5.91976	53	53
39.0	5.92065	41	41
40.0	5.921389	46	46
41.0	5.922004	58	58
42.0	5.922515	38	38
43.0	5.92294	43	43
44.0	5.923293	37	37
45.0	5.923587	23	23
46.0	5.923831	34	34
47.0	5.924033	28	28
48.0	5.924202	26	26
49.0	5.924342	27	27
50.0	5.924458	20	20
51.0	5.924555	31	31
52.0	5.924636	38	38
53.0	5.924703	18	18
54.0	5.924758	27	27
55.0	5.924804	30	30
56.0	5.924843	23	23
57.0	5.924875	21	21
58.0	5.924901	21	21
59.0	5.924923	14	14
60.0	5.924942	17	17
61.0	5.924957	16	16
62.0	5.92497	19	19
63.0	5.92498	9	9
64.0	5.924989	12	12
65.0	5.924996	10	10
66.0	5.925002	13	13
67.0	5.925007	11	11
68.0	5.925011	17	17
69.0	5.925015	14	14
70.0	5.925018	13	13
71.0	5.92502	10	10
72.0	5.925022	13	13
73.0	5.925024	11	11
74.0	5.925025	9	9
75.0	5.925026	6	6
76.0	5.925027	7	7
77.0	5.925028	8	8
78.0	5.925029	17	17
79.0	5.925029	6	6
80.0	5.92503	10	10
81.0	5.92503	5	5
82.0	5.92503	11	11
83.0	5.925031	18	18
84.0	5.925031	15	15
85.0	5.925031	13	13
86.0	5.925031	10	10
87.0	5.925031	5	5
88.0	5.925032	13	13
89.0	5.925032	10	10
90.0	5.925032	9	9
91.0	5.925032	18	18
92.0	5.925032	3	3
93.0	5.925032	10	10
94.0	5.925032	10	10
95.0	5.925032	9	9
96.0	5.925032	6	6
97.0	5.925032	9	9
98.0	5.925032	10	10
99.0	5.925032	9	9
100.0	5.925032	5	5
101.0	0	15	15
102.0	0	7	7
103.0	0	5	5
104.0	0	8	8
105.0	0	2	2
106.0	0	9	9
107.0	0	10	10
108.0	0	5	5
109.0	0	4	4
110.0	0	9	9
111.0	0	6	6
112.0	0	7	7
113.0	0	7	7
114.0	0	6	6
115.0	0	4	4
116.0	0	7	7
117.0	0	2	2
118.0	0	9	9
119.0	0	2	2
120.0	0	8	8
121.0	0	6	6
122.0	0	5	5
123.0	0	4	4
124.0	0	3	3
125.0	0	1	1
126.0	0	7	7
127.0	0	4	4
128.0	0	3	3
129.0	0	6	6
130.0	0	3	3
131.0	0	6	6
132.0	0	6	6
133.0	0	3	3
134.0	0	2	2
135.0	0	3	3
136.0	0	4	4
137.0	0	3	3
138.0	0	6	6
139.0	0	3	3
140.0	0	1	1
141.0	0	5	5
142.0	0	4	4
143.0	0	6	6
144.0	0	3	3
145.0	0	7	7
146.0	0	5	5
147.0	0	2	2
148.0	0	7	7
149.0	0	4	4
150.0	0	1	1
151.0	0	2	2
152.0	0	2	2
153.0	0	4	4
154.0	0	5	5
155.0	0	2	2
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	6	6
160.0	0	4	4
161.0	0	1	1
162.0	0	1	1
163.0	0	3	3
164.0	0	5	5
165.0	0	1	1
166.0	0	2	2
167.0	0	3	3
168.0	0	4	4
169.0	0	1	1
170.0	0	4	4
171.0	0	2	2
172.0	0	1	1
173.0	0	4	4
174.0	0	2	2
175.0	0	2	2
177.0	0	5	5
178.0	0	2	2
179.0	0	5	5
180.0	0	2	2
181.0	0	2	2
183.0	0	4	4
186.0	0	1	1
187.0	0	2	2
188.0	0	5	5
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	6	6
193.0	0	1	1
194.0	0	5	5
195.0	0	1	1
196.0	0	3	3
197.0	0	1	1
198.0	0	1	1
200.0	0	1	1
201.0	0	2	2
202.0	0	2	2
203.0	0	2	2
204.0	0	3	3
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
209.0	0	1	1
210.0	0	2	2
213.0	0	1	1
215.0	0	1	1
216.0	0	2	2
217.0	0	1	1
219.0	0	1	1
220.0	0	2	2
221.0	0	1	1
222.0	0	1	1
223.0	0	2	2
226.0	0	1	1
229.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	2	2
237.0	0	1	1
238.0	0	1	1
240.0	0	1	1
243.0	0	1	1
246.0	0	1	1
247.0	0	1	1
251.0	0	1	1
253.0	0	2	2
255.0	0	1	1
256.0	0	1	1
264.0	0	2	2
266.0	0	1	1
268.0	0	2	2
270.0	0	2	2
271.0	0	1	1
272.0	0	2	2
278.0	0	1	1
279.0	0	1	1
280.0	0	2	2
282.0	0	1	1
283.0	0	1	1
285.0	0	1	1
287.0	0	1	1
293.0	0	2	2
294.0	0	1	1
295.0	0	2	2
296.0	0	2	2
299.0	0	1	1
300.0	0	1	1
301.0	0	1	1
303.0	0	1	1
308.0	0	1	1
310.0	0	2	2
314.0	0	1	1
317.0	0	1	1
320.0	0	1	1
322.0	0	1	1
323.0	0	1	1
325.0	0	1	1
326.0	0	1	1
327.0	0	1	1
329.0	0	2	2
330.0	0	1	1
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
341.0	0	1	1
343.0	0	1	1
344.0	0	1	1
346.0	0	2	2
349.0	0	1	1
350.0	0	1	1
351.0	0	1	1
358.0	0	1	1
359.0	0	1	1
366.0	0	1	1
374.0	0	1	1
375.0	0	2	2
376.0	0	2	2
378.0	0	1	1
379.0	0	1	1
383.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	2	2
390.0	0	1	1
392.0	0	1	1
400.0	0	1	1
409.0	0	1	1
414.0	0	1	1
416.0	0	1	1
417.0	0	2	2
418.0	0	1	1
421.0	0	1	1
426.0	0	1	1
433.0	0	1	1
436.0	0	1	1
439.0	0	1	1
448.0	0	1	1
449.0	0	1	1
461.0	0	1	1
471.0	0	2	2
484.0	0	1	1
496.0	0	1	1
502.0	0	1	1
505.0	0	1	1
523.0	0	1	1
525.0	0	1	1
527.0	0	2	2
531.0	0	1	1
535.0	0	1	1
536.0	0	1	1
550.0	0	1	1
574.0	0	1	1
582.0	0	1	1
599.0	0	1	1
611.0	0	1	1
612.0	0	1	1
623.0	0	1	1
647.0	0	1	1
669.0	0	1	1
763.0	0	1	1
778.0	0	1	1
789.0	0	1	1
794.0	0	1	1
880.0	0	1	1
927.0	0	1	1
929.0	0	1	1
940.0	0	1	1
1002.0	0	1	1
1033.0	0	1	1
1146.0	0	1	1
1169.0	0	1	1
1319.0	0	1	1
1358.0	0	1	1
1485.0	0	1	1
1777.0	0	1	1
2771.0	0	1	1
6157.0	0	1	1