## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-10-05/RU_Nov_Val_1_2015-10-05.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-10-05/RU_Nov_Val_1_2015-10-05.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2015-10-05/RU_Nov_Val_1_2015-10-05.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 08:51:04 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	9366692	33118411	0	0	3581108	3146170	0	0.130595	163088089

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26849335	26849335
2.0	1.816221	2578960	2578960
3.0	2.482437	212601	212601
4.0	3.026216	17402	17402
5.0	3.470059	1971	1971
6.0	3.832334	585	585
7.0	4.12803	343	343
8.0	4.369382	257	257
9.0	4.56638	243	243
10.0	4.727173	210	210
11.0	4.858416	163	163
12.0	4.965539	164	164
13.0	5.052975	141	141
14.0	5.124342	120	120
15.0	5.182593	128	128
16.0	5.230139	113	113
17.0	5.268947	96	96
18.0	5.300623	103	103
19.0	5.326477	83	83
20.0	5.34758	80	80
21.0	5.364805	56	56
22.0	5.378864	70	70
23.0	5.390339	57	57
24.0	5.399705	52	52
25.0	5.40735	38	38
26.0	5.413591	51	51
27.0	5.418684	37	37
28.0	5.422841	37	37
29.0	5.426234	48	48
30.0	5.429004	38	38
31.0	5.431264	28	28
32.0	5.43311	35	35
33.0	5.434616	26	26
34.0	5.435845	27	27
35.0	5.436848	21	21
36.0	5.437667	22	22
37.0	5.438336	28	28
38.0	5.438881	20	20
39.0	5.439327	22	22
40.0	5.43969	22	22
41.0	5.439987	13	13
42.0	5.440229	21	21
43.0	5.440427	15	15
44.0	5.440588	19	19
45.0	5.44072	12	12
46.0	5.440827	24	24
47.0	5.440915	19	19
48.0	5.440986	11	11
49.0	5.441045	18	18
50.0	5.441093	14	14
51.0	5.441132	13	13
52.0	5.441163	9	9
53.0	5.441189	14	14
54.0	5.44121	9	9
55.0	5.441228	12	12
56.0	5.441242	13	13
57.0	5.441253	10	10
58.0	5.441263	7	7
59.0	5.44127	13	13
60.0	5.441277	9	9
61.0	5.441282	6	6
62.0	5.441286	8	8
63.0	5.441289	3	3
64.0	5.441292	7	7
65.0	5.441294	4	4
66.0	5.441296	7	7
67.0	5.441298	5	5
68.0	5.441299	6	6
69.0	5.4413	5	5
70.0	5.441301	7	7
71.0	5.441301	8	8
72.0	5.441302	2	2
73.0	5.441302	5	5
74.0	5.441303	2	2
75.0	5.441303	6	6
76.0	5.441303	5	5
77.0	5.441304	2	2
78.0	5.441304	4	4
79.0	5.441304	2	2
80.0	5.441304	5	5
81.0	5.441304	2	2
82.0	5.441304	5	5
83.0	5.441304	2	2
84.0	5.441304	3	3
85.0	5.441304	3	3
86.0	5.441304	3	3
87.0	5.441304	4	4
88.0	5.441304	3	3
89.0	5.441304	2	2
90.0	5.441304	3	3
91.0	5.441304	4	4
92.0	5.441304	3	3
93.0	5.441304	1	1
94.0	5.441304	2	2
95.0	5.441304	1	1
96.0	5.441304	2	2
97.0	5.441304	5	5
98.0	5.441304	4	4
99.0	5.441304	0	0
100.0	5.441304	3	3
101.0	0	2	2
102.0	0	2	2
105.0	0	1	1
107.0	0	3	3
108.0	0	2	2
110.0	0	1	1
111.0	0	4	4
113.0	0	3	3
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
117.0	0	2	2
118.0	0	3	3
119.0	0	1	1
121.0	0	2	2
122.0	0	3	3
124.0	0	1	1
125.0	0	1	1
126.0	0	4	4
127.0	0	1	1
130.0	0	1	1
131.0	0	1	1
134.0	0	2	2
136.0	0	1	1
140.0	0	2	2
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
148.0	0	1	1
150.0	0	1	1
151.0	0	1	1
153.0	0	1	1
164.0	0	3	3
166.0	0	2	2
170.0	0	1	1
173.0	0	1	1
176.0	0	1	1
181.0	0	1	1
186.0	0	1	1
195.0	0	1	1
203.0	0	1	1
249.0	0	1	1
286.0	0	1	1
330.0	0	1	1