## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-11-25/DK_Mid_Kar_1_2014-11-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-11-25/DK_Mid_Kar_1_2014-11-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-11-25/DK_Mid_Kar_1_2014-11-25.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 08:10:58 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	5231914	16256413	0	0	995269	495425	0	0.05262	261264588

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15083583	15083583
2.0	1.939674	355012	355012
3.0	2.822662	7282	7282
4.0	3.652383	667	667
5.0	4.43205	339	339
6.0	5.164683	262	262
7.0	5.85312	206	206
8.0	6.500026	148	148
9.0	7.107906	158	158
10.0	7.679117	128	128
11.0	8.215868	95	95
12.0	8.720239	82	82
13.0	9.194184	103	103
14.0	9.639538	77	77
15.0	10.058025	52	52
16.0	10.451267	66	66
17.0	10.820786	75	75
18.0	11.168014	70	70
19.0	11.494295	64	64
20.0	11.800893	43	43
21.0	12.088995	53	53
22.0	12.359717	41	41
23.0	12.614107	37	37
24.0	12.853152	35	35
25.0	13.077775	31	31
26.0	13.288848	33	33
27.0	13.487188	32	32
28.0	13.673563	22	22
29.0	13.848695	27	27
30.0	14.013262	20	20
31.0	14.167901	32	32
32.0	14.313211	22	22
33.0	14.449756	24	24
34.0	14.578063	28	28
35.0	14.69863	22	22
36.0	14.811924	19	19
37.0	14.918383	17	17
38.0	15.01842	21	21
39.0	15.112423	23	23
40.0	15.200754	21	21
41.0	15.283757	11	11
42.0	15.361752	13	13
43.0	15.435043	22	22
44.0	15.503912	12	12
45.0	15.568626	16	16
46.0	15.629437	10	10
47.0	15.686579	11	11
48.0	15.740274	8	8
49.0	15.79073	12	12
50.0	15.838142	17	17
51.0	15.882694	12	12
52.0	15.924558	13	13
53.0	15.963897	6	6
54.0	16.000862	8	8
55.0	16.035598	18	18
56.0	16.068238	11	11
57.0	16.098909	7	7
58.0	16.12773	9	9
59.0	16.154812	9	9
60.0	16.180261	11	11
61.0	16.204174	3	3
62.0	16.226645	2	2
63.0	16.24776	9	9
64.0	16.267601	8	8
65.0	16.286246	8	8
66.0	16.303765	7	7
67.0	16.320228	6	6
68.0	16.335698	3	3
69.0	16.350234	8	8
70.0	16.363894	6	6
71.0	16.376729	11	11
72.0	16.38879	6	6
73.0	16.400124	5	5
74.0	16.410774	3	3
75.0	16.420781	4	4
76.0	16.430185	1	1
77.0	16.439021	9	9
78.0	16.447325	5	5
79.0	16.455127	9	9
80.0	16.462459	8	8
81.0	16.469348	5	5
82.0	16.475822	6	6
83.0	16.481905	5	5
84.0	16.487622	6	6
85.0	16.492993	5	5
86.0	16.498041	6	6
87.0	16.502784	6	6
88.0	16.50724	5	5
89.0	16.511428	4	4
90.0	16.515364	6	6
91.0	16.519062	0	0
92.0	16.522537	2	2
93.0	16.525802	5	5
94.0	16.52887	7	7
95.0	16.531753	1	1
96.0	16.534462	5	5
97.0	16.537008	0	0
98.0	16.5394	3	3
99.0	16.541648	3	3
100.0	16.543761	5	5
101.0	0	8	8
102.0	0	4	4
104.0	0	6	6
105.0	0	2	2
106.0	0	3	3
107.0	0	2	2
108.0	0	3	3
109.0	0	2	2
110.0	0	2	2
111.0	0	2	2
112.0	0	2	2
113.0	0	3	3
114.0	0	3	3
115.0	0	3	3
116.0	0	3	3
117.0	0	2	2
118.0	0	4	4
119.0	0	1	1
120.0	0	3	3
121.0	0	3	3
122.0	0	3	3
123.0	0	2	2
124.0	0	6	6
125.0	0	3	3
126.0	0	1	1
127.0	0	6	6
128.0	0	7	7
129.0	0	3	3
130.0	0	2	2
131.0	0	3	3
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	3	3
136.0	0	1	1
137.0	0	3	3
138.0	0	1	1
139.0	0	2	2
140.0	0	2	2
141.0	0	2	2
142.0	0	2	2
143.0	0	5	5
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
148.0	0	3	3
149.0	0	2	2
150.0	0	2	2
151.0	0	4	4
152.0	0	1	1
153.0	0	1	1
154.0	0	1	1
156.0	0	1	1
158.0	0	3	3
159.0	0	3	3
161.0	0	1	1
162.0	0	2	2
163.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
171.0	0	3	3
172.0	0	1	1
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	4	4
177.0	0	1	1
178.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	3	3
186.0	0	2	2
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
191.0	0	1	1
192.0	0	2	2
193.0	0	3	3
194.0	0	4	4
195.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	2	2
201.0	0	1	1
202.0	0	1	1
204.0	0	3	3
205.0	0	1	1
206.0	0	2	2
207.0	0	2	2
208.0	0	1	1
209.0	0	3	3
210.0	0	1	1
211.0	0	1	1
214.0	0	2	2
215.0	0	1	1
217.0	0	1	1
218.0	0	2	2
220.0	0	2	2
221.0	0	1	1
223.0	0	2	2
224.0	0	1	1
226.0	0	2	2
228.0	0	1	1
231.0	0	1	1
233.0	0	1	1
236.0	0	2	2
237.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	2	2
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
252.0	0	1	1
258.0	0	1	1
261.0	0	1	1
263.0	0	1	1
265.0	0	1	1
268.0	0	1	1
269.0	0	1	1
272.0	0	1	1
275.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
280.0	0	1	1
281.0	0	2	2
288.0	0	2	2
290.0	0	1	1
291.0	0	1	1
297.0	0	1	1
305.0	0	2	2
311.0	0	1	1
312.0	0	1	1
318.0	0	1	1
321.0	0	1	1
324.0	0	1	1
327.0	0	2	2
333.0	0	1	1
335.0	0	1	1
336.0	0	1	1
337.0	0	1	1
342.0	0	1	1
344.0	0	1	1
346.0	0	1	1
347.0	0	1	1
349.0	0	1	1
352.0	0	1	1
357.0	0	1	1
359.0	0	1	1
364.0	0	1	1
376.0	0	1	1
395.0	0	1	1
398.0	0	2	2
406.0	0	1	1
408.0	0	1	1
410.0	0	1	1
411.0	0	1	1
438.0	0	1	1
440.0	0	1	1
450.0	0	1	1
459.0	0	1	1
462.0	0	1	1
475.0	0	1	1
482.0	0	1	1
488.0	0	1	1
512.0	0	1	1
522.0	0	1	1
540.0	0	1	1
551.0	0	1	1
581.0	0	1	1
651.0	0	1	1
661.0	0	1	1
702.0	0	1	1