## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-07-24/DE_Bad_Bro_1_2016-07-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-07-24/DE_Bad_Bro_1_2016-07-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-07-24/DE_Bad_Bro_1_2016-07-24.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 08:48:50 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	26938505	12524109	0	0	6199800	972877	0	0.156685	76382008

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10512919	10512919
2.0	1.84877	710354	710354
3.0	2.569181	52910	52910
4.0	3.180645	5734	5734
5.0	3.699636	1654	1654
6.0	4.140141	901	901
7.0	4.514029	634	634
8.0	4.831373	443	443
9.0	5.100726	349	349
10.0	5.329344	293	293
11.0	5.523389	257	257
12.0	5.688088	236	236
13.0	5.82788	190	190
14.0	5.946531	194	194
15.0	6.047239	165	165
16.0	6.132716	157	157
17.0	6.205267	127	127
18.0	6.266846	137	137
19.0	6.319113	102	102
20.0	6.363475	102	102
21.0	6.401128	96	96
22.0	6.433087	99	99
23.0	6.460213	77	77
24.0	6.483237	86	86
25.0	6.502778	69	69
26.0	6.519365	60	60
27.0	6.533443	57	57
28.0	6.545392	46	46
29.0	6.555534	37	37
30.0	6.564142	34	34
31.0	6.571449	27	27
32.0	6.57765	41	41
33.0	6.582914	31	31
34.0	6.587381	28	28
35.0	6.591173	33	33
36.0	6.594392	22	22
37.0	6.597124	22	22
38.0	6.599442	24	24
39.0	6.60141	22	22
40.0	6.603081	18	18
41.0	6.604498	20	20
42.0	6.605702	28	28
43.0	6.606723	24	24
44.0	6.60759	28	28
45.0	6.608326	19	19
46.0	6.60895	21	21
47.0	6.60948	20	20
48.0	6.60993	18	18
49.0	6.610312	17	17
50.0	6.610636	26	26
51.0	6.610911	19	19
52.0	6.611145	20	20
53.0	6.611343	17	17
54.0	6.611511	15	15
55.0	6.611654	20	20
56.0	6.611775	18	18
57.0	6.611878	19	19
58.0	6.611966	18	18
59.0	6.61204	16	16
60.0	6.612103	19	19
61.0	6.612156	8	8
62.0	6.612201	14	14
63.0	6.61224	13	13
64.0	6.612272	10	10
65.0	6.6123	11	11
66.0	6.612324	16	16
67.0	6.612344	13	13
68.0	6.61236	9	9
69.0	6.612375	6	6
70.0	6.612387	9	9
71.0	6.612397	14	14
72.0	6.612406	15	15
73.0	6.612414	11	11
74.0	6.61242	6	6
75.0	6.612425	4	4
76.0	6.61243	5	5
77.0	6.612434	12	12
78.0	6.612437	6	6
79.0	6.61244	5	5
80.0	6.612442	6	6
81.0	6.612444	9	9
82.0	6.612446	6	6
83.0	6.612447	6	6
84.0	6.612449	3	3
85.0	6.61245	10	10
86.0	6.612451	7	7
87.0	6.612451	3	3
88.0	6.612452	5	5
89.0	6.612452	8	8
90.0	6.612453	3	3
91.0	6.612453	3	3
92.0	6.612454	2	2
93.0	6.612454	2	2
94.0	6.612454	5	5
95.0	6.612454	2	2
96.0	6.612455	7	7
97.0	6.612455	1	1
98.0	6.612455	2	2
99.0	6.612455	6	6
100.0	6.612455	4	4
101.0	0	1	1
102.0	0	3	3
103.0	0	2	2
104.0	0	4	4
105.0	0	2	2
106.0	0	5	5
107.0	0	1	1
108.0	0	1	1
109.0	0	2	2
111.0	0	3	3
112.0	0	1	1
114.0	0	1	1
115.0	0	2	2
116.0	0	3	3
118.0	0	2	2
120.0	0	2	2
122.0	0	2	2
123.0	0	1	1
124.0	0	1	1
125.0	0	4	4
127.0	0	1	1
128.0	0	3	3
129.0	0	2	2
130.0	0	2	2
131.0	0	5	5
132.0	0	1	1
133.0	0	1	1
134.0	0	3	3
135.0	0	1	1
137.0	0	1	1
138.0	0	1	1
140.0	0	1	1
141.0	0	3	3
143.0	0	3	3
144.0	0	2	2
145.0	0	2	2
147.0	0	1	1
148.0	0	1	1
151.0	0	2	2
152.0	0	1	1
154.0	0	3	3
155.0	0	1	1
157.0	0	1	1
158.0	0	1	1
160.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
168.0	0	2	2
169.0	0	1	1
177.0	0	1	1
178.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
185.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
203.0	0	2	2
204.0	0	1	1
205.0	0	1	1
207.0	0	1	1
209.0	0	1	1
213.0	0	1	1
215.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
223.0	0	1	1
224.0	0	1	1
233.0	0	1	1
235.0	0	1	1
237.0	0	1	1
238.0	0	2	2
242.0	0	1	1
248.0	0	1	1
250.0	0	1	1
257.0	0	1	1
258.0	0	1	1
260.0	0	1	1
267.0	0	1	1
273.0	0	1	1
275.0	0	1	1
296.0	0	1	1
302.0	0	1	1
312.0	0	1	1
319.0	0	1	1
379.0	0	1	1
399.0	0	1	1
456.0	0	1	1
467.0	0	1	1
488.0	0	1	1
535.0	0	1	1
596.0	0	1	1
685.0	0	1	1
1004.0	0	1	1