## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2016-10-15/RU_Vla_Ale_1_2016-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2016-10-15/RU_Vla_Ale_1_2016-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2016-10-15/RU_Vla_Ale_1_2016-10-15.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 08:54:58 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	30070562	11209310	0	0	7359752	956722	0	0.176669	61874063

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9279497	9279497
2.0	1.834299	621577	621577
3.0	2.530354	48229	48229
4.0	3.111072	5995	5995
5.0	3.595565	1987	1987
6.0	3.999776	1137	1137
7.0	4.33701	804	804
8.0	4.618363	579	579
9.0	4.853096	404	404
10.0	5.048934	326	326
11.0	5.212321	293	293
12.0	5.348635	250	250
13.0	5.462361	201	201
14.0	5.557243	191	191
15.0	5.636403	142	142
16.0	5.702446	135	135
17.0	5.757545	128	128
18.0	5.803515	122	122
19.0	5.841867	110	110
20.0	5.873865	122	122
21.0	5.90056	104	104
22.0	5.922832	115	115
23.0	5.941413	93	93
24.0	5.956916	94	94
25.0	5.969849	103	103
26.0	5.98064	90	90
27.0	5.989643	74	74
28.0	5.997153	80	80
29.0	6.00342	76	76
30.0	6.008648	72	72
31.0	6.013009	52	52
32.0	6.016648	63	63
33.0	6.019684	46	46
34.0	6.022217	36	36
35.0	6.02433	54	54
36.0	6.026093	43	43
37.0	6.027564	36	36
38.0	6.028791	33	33
39.0	6.029815	26	26
40.0	6.030669	32	32
41.0	6.031382	32	32
42.0	6.031977	34	34
43.0	6.032473	30	30
44.0	6.032887	30	30
45.0	6.033232	21	21
46.0	6.03352	24	24
47.0	6.03376	22	22
48.0	6.033961	15	15
49.0	6.034128	18	18
50.0	6.034268	18	18
51.0	6.034384	14	14
52.0	6.034481	29	29
53.0	6.034562	16	16
54.0	6.03463	19	19
55.0	6.034686	18	18
56.0	6.034733	14	14
57.0	6.034772	14	14
58.0	6.034805	13	13
59.0	6.034833	18	18
60.0	6.034855	10	10
61.0	6.034874	20	20
62.0	6.03489	8	8
63.0	6.034904	9	9
64.0	6.034915	12	12
65.0	6.034924	10	10
66.0	6.034931	10	10
67.0	6.034938	12	12
68.0	6.034943	14	14
69.0	6.034948	10	10
70.0	6.034951	15	15
71.0	6.034955	13	13
72.0	6.034957	9	9
73.0	6.034959	12	12
74.0	6.034961	19	19
75.0	6.034963	9	9
76.0	6.034964	8	8
77.0	6.034965	7	7
78.0	6.034966	10	10
79.0	6.034967	4	4
80.0	6.034967	10	10
81.0	6.034968	9	9
82.0	6.034968	13	13
83.0	6.034968	9	9
84.0	6.034969	9	9
85.0	6.034969	12	12
86.0	6.034969	11	11
87.0	6.034969	6	6
88.0	6.034969	9	9
89.0	6.03497	8	8
90.0	6.03497	10	10
91.0	6.03497	7	7
92.0	6.03497	8	8
93.0	6.03497	10	10
94.0	6.03497	8	8
95.0	6.03497	13	13
96.0	6.03497	7	7
97.0	6.03497	16	16
98.0	6.03497	12	12
99.0	6.03497	3	3
100.0	6.03497	11	11
101.0	0	9	9
102.0	0	5	5
103.0	0	7	7
104.0	0	7	7
105.0	0	5	5
106.0	0	7	7
107.0	0	5	5
109.0	0	6	6
110.0	0	8	8
111.0	0	8	8
112.0	0	5	5
113.0	0	5	5
114.0	0	6	6
115.0	0	7	7
116.0	0	5	5
117.0	0	7	7
118.0	0	6	6
119.0	0	8	8
120.0	0	3	3
121.0	0	4	4
122.0	0	1	1
123.0	0	5	5
124.0	0	3	3
125.0	0	4	4
126.0	0	2	2
127.0	0	5	5
128.0	0	4	4
129.0	0	3	3
130.0	0	3	3
131.0	0	5	5
133.0	0	1	1
134.0	0	4	4
136.0	0	1	1
137.0	0	5	5
138.0	0	6	6
139.0	0	1	1
140.0	0	5	5
141.0	0	3	3
142.0	0	3	3
143.0	0	3	3
144.0	0	2	2
145.0	0	3	3
146.0	0	3	3
147.0	0	1	1
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
152.0	0	2	2
153.0	0	4	4
154.0	0	1	1
155.0	0	2	2
156.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	3	3
161.0	0	2	2
162.0	0	1	1
163.0	0	2	2
165.0	0	1	1
166.0	0	3	3
167.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	3	3
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	3	3
177.0	0	1	1
179.0	0	2	2
181.0	0	2	2
182.0	0	3	3
183.0	0	2	2
184.0	0	3	3
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
190.0	0	1	1
191.0	0	2	2
193.0	0	1	1
194.0	0	2	2
195.0	0	2	2
196.0	0	2	2
197.0	0	2	2
199.0	0	1	1
200.0	0	1	1
201.0	0	2	2
202.0	0	2	2
204.0	0	2	2
205.0	0	1	1
208.0	0	1	1
210.0	0	1	1
211.0	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
219.0	0	1	1
221.0	0	1	1
223.0	0	2	2
224.0	0	1	1
226.0	0	2	2
233.0	0	1	1
237.0	0	1	1
239.0	0	1	1
240.0	0	1	1
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
248.0	0	1	1
252.0	0	1	1
257.0	0	1	1
260.0	0	2	2
262.0	0	1	1
263.0	0	1	1
265.0	0	3	3
267.0	0	1	1
268.0	0	1	1
271.0	0	1	1
273.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	1	1
283.0	0	1	1
288.0	0	1	1
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	2	2
298.0	0	1	1
301.0	0	1	1
302.0	0	1	1
303.0	0	1	1
305.0	0	1	1
313.0	0	1	1
320.0	0	1	1
321.0	0	1	1
322.0	0	2	2
325.0	0	1	1
329.0	0	1	1
332.0	0	1	1
336.0	0	1	1
342.0	0	1	1
346.0	0	1	1
350.0	0	1	1
352.0	0	1	1
356.0	0	1	1
358.0	0	1	1
363.0	0	1	1
367.0	0	1	1
369.0	0	1	1
373.0	0	1	1
378.0	0	1	1
380.0	0	1	1
390.0	0	1	1
399.0	0	1	1
405.0	0	1	1
406.0	0	1	1
413.0	0	1	1
421.0	0	2	2
423.0	0	1	1
436.0	0	1	1
453.0	0	1	1
457.0	0	1	1
481.0	0	1	1
492.0	0	1	1
498.0	0	1	1
509.0	0	1	1
610.0	0	1	1
660.0	0	1	1
687.0	0	1	1
690.0	0	1	1
701.0	0	1	1
853.0	0	1	1
908.0	0	1	1
944.0	0	1	1
1076.0	0	1	1
1093.0	0	1	1
1205.0	0	1	1
1299.0	0	1	1
1858.0	0	1	1
3304.0	0	1	1