## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2015-07-01/US_Vir_Cha_1_2015-07-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2015-07-01/US_Vir_Cha_1_2015-07-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2015-07-01/US_Vir_Cha_1_2015-07-01.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 20:24:24 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	2567589	47643107	0	0	1092630	7531476	0	0.165099	134353011

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	32789747	32789747
2.0	1.701446	5462761	5462761
3.0	2.193472	771758	771758
4.0	2.538602	99902	99902
5.0	2.780692	13932	13932
6.0	2.950506	3231	3231
7.0	3.06962	1378	1378
8.0	3.153173	916	916
9.0	3.21178	677	677
10.0	3.25289	493	493
11.0	3.281727	369	369
12.0	3.301954	333	333
13.0	3.316143	280	280
14.0	3.326095	233	233
15.0	3.333076	223	223
16.0	3.337973	182	182
17.0	3.341408	158	158
18.0	3.343817	126	126
19.0	3.345507	114	114
20.0	3.346692	113	113
21.0	3.347524	110	110
22.0	3.348107	91	91
23.0	3.348516	97	97
24.0	3.348803	58	58
25.0	3.349005	77	77
26.0	3.349146	64	64
27.0	3.349245	55	55
28.0	3.349314	43	43
29.0	3.349363	41	41
30.0	3.349397	58	58
31.0	3.349421	61	61
32.0	3.349438	36	36
33.0	3.34945	45	45
34.0	3.349458	47	47
35.0	3.349464	44	44
36.0	3.349468	41	41
37.0	3.349471	30	30
38.0	3.349473	38	38
39.0	3.349474	31	31
40.0	3.349475	17	17
41.0	3.349476	29	29
42.0	3.349476	30	30
43.0	3.349477	20	20
44.0	3.349477	26	26
45.0	3.349477	23	23
46.0	3.349477	21	21
47.0	3.349477	12	12
48.0	3.349478	18	18
49.0	3.349478	14	14
50.0	3.349478	16	16
51.0	3.349478	11	11
52.0	3.349478	10	10
53.0	3.349478	12	12
54.0	3.349478	11	11
55.0	3.349478	17	17
56.0	3.349478	13	13
57.0	3.349478	15	15
58.0	3.349478	9	9
59.0	3.349478	12	12
60.0	3.349478	10	10
61.0	3.349478	9	9
62.0	3.349478	7	7
63.0	3.349478	8	8
64.0	3.349478	10	10
65.0	3.349478	9	9
66.0	3.349478	8	8
67.0	3.349478	8	8
68.0	3.349478	6	6
69.0	3.349478	6	6
70.0	3.349478	8	8
71.0	3.349478	8	8
72.0	3.349478	9	9
73.0	3.349478	3	3
74.0	3.349478	6	6
75.0	3.349478	5	5
76.0	3.349478	3	3
77.0	3.349478	2	2
78.0	3.349478	2	2
79.0	3.349478	6	6
80.0	3.349478	2	2
81.0	3.349478	1	1
82.0	3.349478	1	1
83.0	3.349478	2	2
84.0	3.349478	5	5
85.0	3.349478	9	9
86.0	3.349478	6	6
87.0	3.349478	3	3
88.0	3.349478	2	2
89.0	3.349478	2	2
90.0	3.349478	6	6
91.0	3.349478	3	3
92.0	3.349478	3	3
93.0	3.349478	3	3
94.0	3.349478	7	7
95.0	3.349478	6	6
96.0	3.349478	3	3
97.0	3.349478	3	3
98.0	3.349478	5	5
99.0	3.349478	5	5
100.0	3.349478	7	7
101.0	0	4	4
102.0	0	3	3
103.0	0	4	4
104.0	0	2	2
105.0	0	2	2
106.0	0	2	2
107.0	0	6	6
108.0	0	1	1
109.0	0	1	1
110.0	0	1	1
111.0	0	2	2
112.0	0	2	2
113.0	0	1	1
117.0	0	3	3
118.0	0	3	3
119.0	0	3	3
120.0	0	1	1
122.0	0	3	3
123.0	0	2	2
124.0	0	1	1
126.0	0	1	1
127.0	0	2	2
128.0	0	3	3
129.0	0	1	1
130.0	0	2	2
131.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
137.0	0	3	3
139.0	0	2	2
140.0	0	5	5
142.0	0	1	1
143.0	0	3	3
144.0	0	2	2
146.0	0	4	4
151.0	0	1	1
153.0	0	3	3
154.0	0	3	3
157.0	0	2	2
158.0	0	3	3
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
163.0	0	1	1
169.0	0	3	3
170.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
175.0	0	2	2
176.0	0	2	2
177.0	0	4	4
178.0	0	2	2
179.0	0	1	1
180.0	0	2	2
181.0	0	1	1
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
190.0	0	3	3
191.0	0	2	2
193.0	0	1	1
194.0	0	3	3
195.0	0	2	2
196.0	0	2	2
197.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
210.0	0	2	2
212.0	0	1	1
214.0	0	2	2
218.0	0	3	3
221.0	0	2	2
222.0	0	1	1
224.0	0	3	3
229.0	0	1	1
230.0	0	1	1
232.0	0	1	1
234.0	0	1	1
235.0	0	2	2
238.0	0	1	1
241.0	0	1	1
243.0	0	1	1
247.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	1	1
262.0	0	1	1
265.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	2	2
274.0	0	1	1
275.0	0	1	1
277.0	0	1	1
291.0	0	1	1
293.0	0	1	1
295.0	0	1	1
297.0	0	1	1
298.0	0	1	1
302.0	0	2	2
316.0	0	1	1
318.0	0	1	1
320.0	0	3	3
328.0	0	1	1
335.0	0	1	1
337.0	0	1	1
339.0	0	1	1
342.0	0	1	1
357.0	0	1	1
359.0	0	1	1
377.0	0	1	1
390.0	0	1	1
446.0	0	1	1
459.0	0	1	1
490.0	0	1	1
543.0	0	1	1
552.0	0	1	1
557.0	0	1	1