## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2016-08-18/UA_Kha_Kha_1_2016-08-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2016-08-18/UA_Kha_Kha_1_2016-08-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2016-08-18/UA_Kha_Kha_1_2016-08-18.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 08:42:44 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	31178764	7558436	0	0	7234856	645354	0	0.184155	41705430

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	6271530	6271530
2.0	1.83424	355569	355569
3.0	2.530197	27382	27382
4.0	3.110792	4142	4142
5.0	3.595148	1719	1719
6.0	3.999217	1059	1059
7.0	4.336308	791	791
8.0	4.617523	505	505
9.0	4.852123	404	404
10.0	5.047836	317	317
11.0	5.211108	283	283
12.0	5.347316	242	242
13.0	5.460946	214	214
14.0	5.555741	168	168
15.0	5.634823	150	150
16.0	5.700796	146	146
17.0	5.755833	130	130
18.0	5.801748	119	119
19.0	5.840052	126	126
20.0	5.872006	108	108
21.0	5.898664	102	102
22.0	5.920903	100	100
23.0	5.939455	99	99
24.0	5.954933	94	94
25.0	5.967844	81	81
26.0	5.978616	67	67
27.0	5.987602	79	79
28.0	5.995099	79	79
29.0	6.001352	82	82
30.0	6.00657	55	55
31.0	6.010922	57	57
32.0	6.014553	47	47
33.0	6.017582	51	51
34.0	6.020109	53	53
35.0	6.022217	49	49
36.0	6.023976	47	47
37.0	6.025443	46	46
38.0	6.026667	28	28
39.0	6.027688	36	36
40.0	6.02854	33	33
41.0	6.029251	37	37
42.0	6.029844	24	24
43.0	6.030338	30	30
44.0	6.030751	20	20
45.0	6.031095	24	24
46.0	6.031382	25	25
47.0	6.031622	22	22
48.0	6.031822	25	25
49.0	6.031988	28	28
50.0	6.032127	10	10
51.0	6.032243	19	19
52.0	6.03234	18	18
53.0	6.032421	17	17
54.0	6.032488	12	12
55.0	6.032544	20	20
56.0	6.032591	19	19
57.0	6.03263	15	15
58.0	6.032663	14	14
59.0	6.03269	19	19
60.0	6.032713	8	8
61.0	6.032732	14	14
62.0	6.032748	16	16
63.0	6.032761	9	9
64.0	6.032772	9	9
65.0	6.032781	13	13
66.0	6.032789	10	10
67.0	6.032795	14	14
68.0	6.032801	6	6
69.0	6.032805	13	13
70.0	6.032809	7	7
71.0	6.032812	11	11
72.0	6.032814	11	11
73.0	6.032816	10	10
74.0	6.032818	10	10
75.0	6.03282	9	9
76.0	6.032821	13	13
77.0	6.032822	5	5
78.0	6.032823	13	13
79.0	6.032824	13	13
80.0	6.032824	10	10
81.0	6.032825	5	5
82.0	6.032825	11	11
83.0	6.032826	7	7
84.0	6.032826	16	16
85.0	6.032826	10	10
86.0	6.032826	5	5
87.0	6.032826	6	6
88.0	6.032827	13	13
89.0	6.032827	12	12
90.0	6.032827	5	5
91.0	6.032827	9	9
92.0	6.032827	6	6
93.0	6.032827	11	11
94.0	6.032827	8	8
95.0	6.032827	10	10
96.0	6.032827	11	11
97.0	6.032827	8	8
98.0	6.032827	10	10
99.0	6.032827	3	3
100.0	6.032827	10	10
101.0	0	3	3
102.0	0	5	5
103.0	0	3	3
104.0	0	5	5
105.0	0	3	3
106.0	0	5	5
107.0	0	6	6
108.0	0	4	4
109.0	0	5	5
110.0	0	4	4
111.0	0	9	9
112.0	0	2	2
113.0	0	5	5
114.0	0	7	7
115.0	0	5	5
116.0	0	5	5
117.0	0	6	6
118.0	0	7	7
119.0	0	3	3
120.0	0	2	2
121.0	0	1	1
122.0	0	5	5
123.0	0	6	6
124.0	0	2	2
125.0	0	2	2
127.0	0	2	2
128.0	0	3	3
129.0	0	7	7
130.0	0	1	1
131.0	0	3	3
132.0	0	1	1
133.0	0	4	4
134.0	0	5	5
136.0	0	2	2
137.0	0	2	2
138.0	0	2	2
139.0	0	1	1
140.0	0	5	5
141.0	0	7	7
142.0	0	3	3
143.0	0	4	4
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
147.0	0	3	3
148.0	0	2	2
149.0	0	4	4
151.0	0	6	6
152.0	0	3	3
153.0	0	2	2
154.0	0	1	1
155.0	0	1	1
156.0	0	1	1
157.0	0	4	4
158.0	0	6	6
159.0	0	2	2
161.0	0	3	3
163.0	0	3	3
164.0	0	1	1
165.0	0	4	4
166.0	0	2	2
167.0	0	2	2
169.0	0	3	3
170.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	3	3
180.0	0	2	2
181.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	2	2
194.0	0	2	2
195.0	0	3	3
197.0	0	1	1
198.0	0	1	1
200.0	0	2	2
201.0	0	1	1
204.0	0	1	1
205.0	0	2	2
207.0	0	2	2
208.0	0	1	1
209.0	0	1	1
212.0	0	1	1
214.0	0	1	1
215.0	0	2	2
217.0	0	1	1
219.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
235.0	0	2	2
239.0	0	2	2
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
247.0	0	2	2
248.0	0	1	1
252.0	0	1	1
258.0	0	2	2
260.0	0	4	4
262.0	0	2	2
266.0	0	1	1
267.0	0	2	2
269.0	0	1	1
270.0	0	2	2
271.0	0	1	1
275.0	0	1	1
276.0	0	1	1
278.0	0	1	1
281.0	0	1	1
284.0	0	1	1
288.0	0	1	1
289.0	0	2	2
294.0	0	1	1
296.0	0	1	1
297.0	0	1	1
301.0	0	1	1
306.0	0	1	1
308.0	0	1	1
311.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
320.0	0	1	1
321.0	0	1	1
323.0	0	1	1
324.0	0	1	1
328.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	1	1
340.0	0	1	1
342.0	0	1	1
344.0	0	2	2
348.0	0	2	2
349.0	0	1	1
350.0	0	1	1
351.0	0	1	1
356.0	0	1	1
357.0	0	1	1
361.0	0	1	1
362.0	0	1	1
376.0	0	1	1
380.0	0	1	1
381.0	0	1	1
383.0	0	1	1
387.0	0	1	1
404.0	0	1	1
409.0	0	1	1
421.0	0	1	1
424.0	0	1	1
427.0	0	1	1
429.0	0	1	1
443.0	0	1	1
448.0	0	1	1
458.0	0	1	1
470.0	0	1	1
495.0	0	1	1
505.0	0	1	1
546.0	0	1	1
566.0	0	1	1
573.0	0	1	1
582.0	0	1	1
654.0	0	1	1
664.0	0	1	1
683.0	0	1	1
700.0	0	1	1
733.0	0	1	1
769.0	0	1	1
813.0	0	1	1
831.0	0	1	1
835.0	0	1	1
1035.0	0	1	1
1066.0	0	1	1
1162.0	0	1	1
1297.0	0	1	1
2206.0	0	1	1
4206.0	0	1	1