## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2014-07-31/SE_Ska_Lun_1_2014-07-31.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2014-07-31/SE_Ska_Lun_1_2014-07-31.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2014-07-31/SE_Ska_Lun_1_2014-07-31.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 08:13:32 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	8662963	17968236	0	0	1695271	518488	0	0.061262	305326535

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	16788812	16788812
2.0	1.942849	365332	365332
3.0	2.831813	6616	6616
4.0	3.669972	565	565
5.0	4.460229	325	325
6.0	5.205322	259	259
7.0	5.907832	185	185
8.0	6.570193	153	153
9.0	7.194699	119	119
10.0	7.783514	125	125
11.0	8.338678	92	92
12.0	8.862113	93	93
13.0	9.355634	81	81
14.0	9.820949	62	62
15.0	10.259671	64	64
16.0	10.673319	64	64
17.0	11.063327	49	49
18.0	11.431046	44	44
19.0	11.777749	48	48
20.0	12.104638	45	45
21.0	12.412844	42	42
22.0	12.703437	37	37
23.0	12.977421	23	23
24.0	13.235747	39	39
25.0	13.47931	37	37
26.0	13.708952	31	31
27.0	13.925471	30	30
28.0	14.129615	20	20
29.0	14.322092	26	26
30.0	14.503568	23	23
31.0	14.674673	23	23
32.0	14.836	25	25
33.0	14.988106	19	19
34.0	15.131519	14	14
35.0	15.266736	13	13
36.0	15.394225	25	25
37.0	15.514428	16	16
38.0	15.627762	10	10
39.0	15.734618	19	19
40.0	15.835367	14	14
41.0	15.930358	15	15
42.0	16.019921	18	18
43.0	16.104365	11	11
44.0	16.183983	9	9
45.0	16.25905	9	9
46.0	16.329827	14	14
47.0	16.39656	18	18
48.0	16.459478	19	19
49.0	16.518801	8	8
50.0	16.574733	6	6
51.0	16.627469	16	16
52.0	16.677191	9	9
53.0	16.724071	14	14
54.0	16.768272	12	12
55.0	16.809947	7	7
56.0	16.84924	14	14
57.0	16.886287	12	12
58.0	16.921217	6	6
59.0	16.954151	16	16
60.0	16.985203	10	10
61.0	17.01448	10	10
62.0	17.042083	8	8
63.0	17.068109	7	7
64.0	17.092648	8	8
65.0	17.115784	2	2
66.0	17.137599	5	5
67.0	17.158166	7	7
68.0	17.177558	11	11
69.0	17.195841	6	6
70.0	17.21308	9	9
71.0	17.229334	6	6
72.0	17.244658	5	5
73.0	17.259107	5	5
74.0	17.27273	5	5
75.0	17.285574	4	4
76.0	17.297685	7	7
77.0	17.309103	5	5
78.0	17.319869	4	4
79.0	17.330019	5	5
80.0	17.339589	2	2
81.0	17.348613	7	7
82.0	17.35712	6	6
83.0	17.365142	8	8
84.0	17.372705	5	5
85.0	17.379836	5	5
86.0	17.386559	2	2
87.0	17.392898	1	1
88.0	17.398875	2	2
89.0	17.40451	4	4
90.0	17.409823	4	4
91.0	17.414832	1	1
92.0	17.419555	6	6
93.0	17.424009	0	0
94.0	17.428207	0	0
95.0	17.432166	5	5
96.0	17.435899	7	7
97.0	17.439418	2	2
98.0	17.442736	3	3
99.0	17.445864	1	1
100.0	17.448814	1	1
101.0	0	3	3
102.0	0	3	3
103.0	0	1	1
104.0	0	2	2
105.0	0	3	3
106.0	0	5	5
107.0	0	4	4
108.0	0	4	4
109.0	0	1	1
110.0	0	2	2
111.0	0	4	4
112.0	0	3	3
113.0	0	2	2
114.0	0	2	2
115.0	0	2	2
116.0	0	2	2
117.0	0	3	3
118.0	0	2	2
119.0	0	3	3
120.0	0	5	5
121.0	0	3	3
122.0	0	2	2
123.0	0	5	5
124.0	0	3	3
125.0	0	3	3
126.0	0	2	2
127.0	0	3	3
128.0	0	2	2
129.0	0	3	3
130.0	0	7	7
131.0	0	4	4
132.0	0	1	1
133.0	0	5	5
134.0	0	2	2
135.0	0	3	3
136.0	0	1	1
137.0	0	2	2
138.0	0	2	2
139.0	0	2	2
140.0	0	3	3
141.0	0	2	2
142.0	0	2	2
143.0	0	5	5
144.0	0	3	3
145.0	0	2	2
146.0	0	2	2
148.0	0	2	2
149.0	0	2	2
151.0	0	2	2
152.0	0	3	3
153.0	0	1	1
154.0	0	2	2
155.0	0	2	2
157.0	0	3	3
159.0	0	1	1
161.0	0	2	2
162.0	0	1	1
164.0	0	2	2
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	3	3
171.0	0	1	1
172.0	0	4	4
176.0	0	2	2
177.0	0	2	2
178.0	0	1	1
179.0	0	2	2
180.0	0	4	4
181.0	0	2	2
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
187.0	0	3	3
188.0	0	3	3
189.0	0	1	1
191.0	0	5	5
192.0	0	1	1
193.0	0	1	1
195.0	0	1	1
197.0	0	1	1
198.0	0	4	4
199.0	0	1	1
200.0	0	3	3
201.0	0	2	2
202.0	0	1	1
203.0	0	1	1
204.0	0	2	2
206.0	0	2	2
207.0	0	2	2
208.0	0	1	1
210.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
219.0	0	2	2
220.0	0	2	2
221.0	0	2	2
223.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	2	2
231.0	0	1	1
233.0	0	3	3
235.0	0	1	1
236.0	0	1	1
237.0	0	2	2
241.0	0	1	1
242.0	0	3	3
243.0	0	1	1
246.0	0	3	3
247.0	0	1	1
248.0	0	2	2
249.0	0	1	1
250.0	0	1	1
252.0	0	2	2
254.0	0	1	1
256.0	0	1	1
257.0	0	2	2
260.0	0	2	2
261.0	0	1	1
262.0	0	1	1
263.0	0	1	1
264.0	0	2	2
266.0	0	2	2
267.0	0	2	2
268.0	0	3	3
269.0	0	1	1
270.0	0	2	2
272.0	0	2	2
274.0	0	3	3
278.0	0	1	1
280.0	0	2	2
281.0	0	2	2
284.0	0	1	1
288.0	0	1	1
290.0	0	1	1
295.0	0	1	1
297.0	0	1	1
300.0	0	1	1
306.0	0	1	1
310.0	0	1	1
311.0	0	1	1
313.0	0	2	2
315.0	0	1	1
316.0	0	1	1
323.0	0	1	1
325.0	0	1	1
326.0	0	1	1
328.0	0	1	1
330.0	0	1	1
333.0	0	1	1
336.0	0	3	3
338.0	0	1	1
347.0	0	2	2
349.0	0	1	1
350.0	0	1	1
355.0	0	1	1
357.0	0	1	1
358.0	0	1	1
359.0	0	2	2
360.0	0	1	1
363.0	0	2	2
365.0	0	1	1
369.0	0	2	2
371.0	0	1	1
377.0	0	1	1
380.0	0	2	2
382.0	0	1	1
389.0	0	1	1
390.0	0	1	1
392.0	0	1	1
395.0	0	1	1
396.0	0	1	1
401.0	0	1	1
406.0	0	1	1
422.0	0	1	1
424.0	0	1	1
427.0	0	1	1
430.0	0	1	1
432.0	0	1	1
441.0	0	1	1
443.0	0	1	1
444.0	0	2	2
450.0	0	1	1
452.0	0	1	1
455.0	0	2	2
462.0	0	1	1
475.0	0	1	1
484.0	0	1	1
493.0	0	1	1
494.0	0	1	1
504.0	0	1	1
519.0	0	1	1
570.0	0	1	1
572.0	0	1	1
581.0	0	1	1
582.0	0	1	1
607.0	0	1	1
622.0	0	1	1
645.0	0	1	1
647.0	0	1	1
685.0	0	1	1
743.0	0	1	1
750.0	0	1	1