## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Tul_Tul_1_2015-09-20/RU_Tul_Tul_1_2015-09-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Tul_Tul_1_2015-09-20/RU_Tul_Tul_1_2015-09-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Tul_Tul_1_2015-09-20/RU_Tul_Tul_1_2015-09-20.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 08:57:23 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	9295339	35174918	0	0	3595579	3524791	0	0.133657	163578370

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	28147823	28147823
2.0	1.806514	2902025	2902025
3.0	2.456979	254528	254528
4.0	2.981588	21699	21699
5.0	3.404692	2456	2456
6.0	3.745932	658	658
7.0	4.021146	348	348
8.0	4.243111	231	231
9.0	4.422128	207	207
10.0	4.566508	176	176
11.0	4.682953	122	122
12.0	4.776867	112	112
13.0	4.85261	92	92
14.0	4.913698	70	70
15.0	4.962966	67	67
16.0	5.002701	77	77
17.0	5.034749	55	55
18.0	5.060595	39	39
19.0	5.081441	38	38
20.0	5.098253	48	48
21.0	5.111812	37	37
22.0	5.122748	36	36
23.0	5.131568	28	28
24.0	5.138681	26	26
25.0	5.144418	26	26
26.0	5.149045	17	17
27.0	5.152777	20	20
28.0	5.155787	18	18
29.0	5.158214	15	15
30.0	5.160172	11	11
31.0	5.161751	12	12
32.0	5.163024	17	17
33.0	5.164051	12	12
34.0	5.16488	10	10
35.0	5.165548	12	12
36.0	5.166086	17	17
37.0	5.166521	10	10
38.0	5.166871	3	3
39.0	5.167154	9	9
40.0	5.167382	6	6
41.0	5.167566	10	10
42.0	5.167714	3	3
43.0	5.167834	6	6
44.0	5.16793	9	9
45.0	5.168008	4	4
46.0	5.168071	6	6
47.0	5.168121	6	6
48.0	5.168162	8	8
49.0	5.168195	6	6
50.0	5.168222	6	6
51.0	5.168243	5	5
52.0	5.16826	3	3
53.0	5.168274	4	4
54.0	5.168285	5	5
55.0	5.168294	4	4
56.0	5.168302	2	2
57.0	5.168308	2	2
58.0	5.168312	2	2
59.0	5.168316	2	2
60.0	5.168319	1	1
61.0	5.168322	2	2
62.0	5.168324	3	3
63.0	5.168325	2	2
64.0	5.168327	1	1
65.0	5.168328	3	3
66.0	5.168329	1	1
67.0	5.168329	1	1
68.0	5.16833	1	1
69.0	5.16833	2	2
70.0	5.168331	0	0
71.0	5.168331	2	2
72.0	5.168331	1	1
73.0	5.168331	0	0
74.0	5.168332	0	0
75.0	5.168332	1	1
76.0	5.168332	1	1
77.0	5.168332	3	3
78.0	5.168332	0	0
79.0	5.168332	1	1
80.0	5.168332	0	0
81.0	5.168332	0	0
82.0	5.168332	2	2
83.0	5.168332	1	1
84.0	5.168332	0	0
85.0	5.168332	2	2
86.0	5.168332	0	0
87.0	5.168332	0	0
88.0	5.168332	0	0
89.0	5.168332	2	2
90.0	5.168332	0	0
91.0	5.168332	0	0
92.0	5.168332	1	1
93.0	5.168332	1	1
94.0	5.168332	0	0
95.0	5.168332	1	1
96.0	5.168332	0	0
97.0	5.168332	0	0
98.0	5.168332	0	0
99.0	5.168332	0	0
100.0	5.168332	1	1
105.0	0	1	1
109.0	0	1	1
113.0	0	2	2
116.0	0	1	1
117.0	0	1	1
121.0	0	1	1
122.0	0	1	1
125.0	0	1	1
145.0	0	1	1
146.0	0	2	2
154.0	0	1	1
182.0	0	1	1
210.0	0	1	1
239.0	0	1	1
364.0	0	1	1