## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Lut_1_2014-10-20/GB_Lei_Lut_1_2014-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Lut_1_2014-10-20/GB_Lei_Lut_1_2014-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Lut_1_2014-10-20/GB_Lei_Lut_1_2014-10-20.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 08:34:44 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	5367968	27049997	0	0	1370510	724344	0	0.047407	496021819

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25372079	25372079
2.0	1.946926	531205	531205
3.0	2.843596	8811	8811
4.0	3.692676	696	696
5.0	4.496693	408	408
6.0	5.258037	289	289
7.0	5.978974	221	221
8.0	6.661649	194	194
9.0	7.308091	182	182
10.0	7.920225	170	170
11.0	8.49987	128	128
12.0	9.048751	139	139
13.0	9.568502	117	117
14.0	10.060667	98	98
15.0	10.526712	91	91
16.0	10.968021	85	85
17.0	11.385909	75	75
18.0	11.781618	65	65
19.0	12.156326	65	65
20.0	12.511146	69	69
21.0	12.847135	67	67
22.0	13.165291	58	58
23.0	13.466562	42	42
24.0	13.751843	42	42
25.0	14.021984	34	34
26.0	14.277787	29	29
27.0	14.520014	36	36
28.0	14.749385	27	27
29.0	14.966582	45	45
30.0	15.172252	30	30
31.0	15.367006	31	31
32.0	15.551424	39	39
33.0	15.726055	32	32
34.0	15.891417	32	32
35.0	16.048002	22	22
36.0	16.196277	24	24
37.0	16.336683	30	30
38.0	16.469637	24	24
39.0	16.595534	20	20
40.0	16.71475	30	30
41.0	16.827638	20	20
42.0	16.934535	27	27
43.0	17.035759	29	29
44.0	17.13161	16	16
45.0	17.222374	12	12
46.0	17.308321	19	19
47.0	17.389707	10	10
48.0	17.466773	20	20
49.0	17.539749	14	14
50.0	17.608851	14	14
51.0	17.674287	9	9
52.0	17.736249	19	19
53.0	17.794923	15	15
54.0	17.850483	11	11
55.0	17.903094	13	13
56.0	17.952912	10	10
57.0	18.000087	12	12
58.0	18.044758	13	13
59.0	18.087058	9	9
60.0	18.127113	15	15
61.0	18.165042	13	13
62.0	18.200959	10	10
63.0	18.234969	9	9
64.0	18.267174	13	13
65.0	18.297669	8	8
66.0	18.326546	8	8
67.0	18.353891	11	11
68.0	18.379784	7	7
69.0	18.404303	10	10
70.0	18.427521	13	13
71.0	18.449507	6	6
72.0	18.470325	7	7
73.0	18.490039	3	3
74.0	18.508707	4	4
75.0	18.526383	10	10
76.0	18.543122	7	7
77.0	18.558972	12	12
78.0	18.573981	6	6
79.0	18.588193	3	3
80.0	18.601651	13	13
81.0	18.614395	11	11
82.0	18.626463	4	4
83.0	18.63789	5	5
84.0	18.64871	6	6
85.0	18.658956	4	4
86.0	18.668659	2	2
87.0	18.677846	5	5
88.0	18.686546	2	2
89.0	18.694784	8	8
90.0	18.702585	2	2
91.0	18.709972	6	6
92.0	18.716967	8	8
93.0	18.72359	6	6
94.0	18.729862	5	5
95.0	18.735802	4	4
96.0	18.741426	6	6
97.0	18.746751	5	5
98.0	18.751794	3	3
99.0	18.756569	2	2
100.0	18.761091	7	7
101.0	0	4	4
102.0	0	1	1
103.0	0	1	1
104.0	0	3	3
105.0	0	12	12
106.0	0	2	2
107.0	0	3	3
108.0	0	3	3
109.0	0	4	4
110.0	0	2	2
111.0	0	5	5
112.0	0	2	2
113.0	0	3	3
114.0	0	2	2
115.0	0	4	4
116.0	0	4	4
117.0	0	3	3
118.0	0	5	5
119.0	0	3	3
120.0	0	4	4
121.0	0	4	4
122.0	0	4	4
123.0	0	2	2
124.0	0	1	1
125.0	0	3	3
126.0	0	3	3
127.0	0	5	5
128.0	0	3	3
129.0	0	2	2
130.0	0	2	2
132.0	0	1	1
134.0	0	2	2
135.0	0	2	2
136.0	0	1	1
137.0	0	4	4
138.0	0	2	2
139.0	0	5	5
140.0	0	4	4
141.0	0	2	2
143.0	0	1	1
146.0	0	1	1
147.0	0	5	5
148.0	0	5	5
149.0	0	2	2
150.0	0	1	1
151.0	0	3	3
152.0	0	5	5
153.0	0	2	2
154.0	0	2	2
155.0	0	3	3
156.0	0	1	1
157.0	0	1	1
158.0	0	3	3
159.0	0	5	5
160.0	0	3	3
161.0	0	1	1
162.0	0	2	2
163.0	0	2	2
165.0	0	3	3
166.0	0	2	2
169.0	0	4	4
170.0	0	3	3
172.0	0	2	2
174.0	0	2	2
175.0	0	1	1
176.0	0	2	2
177.0	0	3	3
179.0	0	2	2
180.0	0	1	1
181.0	0	3	3
182.0	0	3	3
183.0	0	4	4
184.0	0	1	1
185.0	0	2	2
186.0	0	3	3
187.0	0	3	3
189.0	0	3	3
190.0	0	1	1
194.0	0	3	3
195.0	0	1	1
197.0	0	3	3
198.0	0	3	3
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
211.0	0	2	2
213.0	0	1	1
217.0	0	1	1
218.0	0	1	1
220.0	0	1	1
221.0	0	2	2
222.0	0	1	1
223.0	0	1	1
225.0	0	1	1
226.0	0	1	1
229.0	0	1	1
231.0	0	1	1
232.0	0	2	2
233.0	0	2	2
234.0	0	3	3
235.0	0	1	1
236.0	0	2	2
238.0	0	4	4
239.0	0	2	2
242.0	0	1	1
245.0	0	1	1
246.0	0	2	2
247.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	2	2
255.0	0	1	1
256.0	0	4	4
258.0	0	1	1
261.0	0	1	1
262.0	0	2	2
263.0	0	1	1
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	3	3
270.0	0	1	1
273.0	0	1	1
274.0	0	1	1
276.0	0	3	3
277.0	0	1	1
281.0	0	1	1
282.0	0	1	1
285.0	0	1	1
288.0	0	2	2
289.0	0	1	1
290.0	0	2	2
295.0	0	1	1
296.0	0	1	1
300.0	0	3	3
301.0	0	1	1
303.0	0	1	1
305.0	0	1	1
310.0	0	1	1
311.0	0	2	2
312.0	0	1	1
314.0	0	2	2
317.0	0	1	1
318.0	0	1	1
324.0	0	2	2
325.0	0	1	1
327.0	0	2	2
328.0	0	2	2
330.0	0	2	2
332.0	0	1	1
335.0	0	1	1
336.0	0	3	3
338.0	0	1	1
344.0	0	2	2
345.0	0	1	1
347.0	0	1	1
350.0	0	1	1
352.0	0	1	1
356.0	0	3	3
357.0	0	1	1
358.0	0	1	1
362.0	0	2	2
363.0	0	1	1
364.0	0	2	2
365.0	0	1	1
369.0	0	1	1
374.0	0	1	1
377.0	0	1	1
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
386.0	0	1	1
389.0	0	2	2
391.0	0	2	2
392.0	0	1	1
393.0	0	2	2
395.0	0	1	1
398.0	0	1	1
399.0	0	1	1
403.0	0	1	1
409.0	0	1	1
415.0	0	1	1
421.0	0	1	1
423.0	0	1	1
438.0	0	1	1
440.0	0	1	1
456.0	0	3	3
457.0	0	1	1
463.0	0	1	1
477.0	0	1	1
486.0	0	1	1
500.0	0	1	1
502.0	0	1	1
511.0	0	1	1
512.0	0	1	1
515.0	0	1	1
518.0	0	1	1
523.0	0	1	1
529.0	0	1	1
554.0	0	1	1
567.0	0	1	1
572.0	0	1	1
573.0	0	1	1
592.0	0	1	1
597.0	0	1	1
610.0	0	1	1
611.0	0	1	1
612.0	0	1	1
615.0	0	1	1
627.0	0	1	1
644.0	0	1	1
701.0	0	1	1
768.0	0	1	1
779.0	0	1	1
838.0	0	1	1
908.0	0	1	1