## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-08/SE_Ska_Lun_1_2015-08-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-08/SE_Ska_Lun_1_2015-08-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-08/SE_Ska_Lun_1_2015-08-08.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 09:07:51 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	11808887	32033953	0	0	4238211	4594151	0	0.176952	100727848

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23183858	23183858
2.0	1.727585	3421294	3421294
3.0	2.256964	462360	462360
4.0	2.642133	58997	58997
5.0	2.922376	7676	7676
6.0	3.126276	1239	1239
7.0	3.274631	434	434
8.0	3.382571	227	227
9.0	3.461107	209	209
10.0	3.518249	174	174
11.0	3.559824	132	132
12.0	3.590074	117	117
13.0	3.612083	102	102
14.0	3.628096	99	99
15.0	3.639748	81	81
16.0	3.648225	86	86
17.0	3.654393	56	56
18.0	3.65888	50	50
19.0	3.662146	46	46
20.0	3.664521	51	51
21.0	3.66625	32	32
22.0	3.667507	20	20
23.0	3.668422	25	25
24.0	3.669088	18	18
25.0	3.669573	25	25
26.0	3.669925	21	21
27.0	3.670182	19	19
28.0	3.670368	17	17
29.0	3.670504	23	23
30.0	3.670603	20	20
31.0	3.670674	9	9
32.0	3.670727	7	7
33.0	3.670765	15	15
34.0	3.670793	10	10
35.0	3.670813	9	9
36.0	3.670827	6	6
37.0	3.670838	15	15
38.0	3.670846	9	9
39.0	3.670851	9	9
40.0	3.670855	7	7
41.0	3.670858	4	4
42.0	3.670861	6	6
43.0	3.670862	5	5
44.0	3.670863	6	6
45.0	3.670864	8	8
46.0	3.670865	2	2
47.0	3.670865	6	6
48.0	3.670866	8	8
49.0	3.670866	4	4
50.0	3.670866	4	4
51.0	3.670866	1	1
52.0	3.670866	2	2
53.0	3.670866	3	3
54.0	3.670866	5	5
55.0	3.670866	3	3
56.0	3.670866	5	5
57.0	3.670866	3	3
58.0	3.670866	1	1
59.0	3.670866	1	1
60.0	3.670866	4	4
61.0	3.670866	3	3
62.0	3.670866	1	1
63.0	3.670866	1	1
64.0	3.670866	2	2
65.0	3.670866	7	7
66.0	3.670866	3	3
67.0	3.670866	1	1
68.0	3.670866	2	2
69.0	3.670866	1	1
70.0	3.670866	1	1
71.0	3.670866	0	0
72.0	3.670866	0	0
73.0	3.670866	1	1
74.0	3.670866	1	1
75.0	3.670866	1	1
76.0	3.670866	0	0
77.0	3.670866	2	2
78.0	3.670866	0	0
79.0	3.670866	0	0
80.0	3.670866	0	0
81.0	3.670866	0	0
82.0	3.670866	0	0
83.0	3.670866	3	3
84.0	3.670866	1	1
85.0	3.670866	0	0
86.0	3.670866	1	1
87.0	3.670866	0	0
88.0	3.670866	0	0
89.0	3.670866	1	1
90.0	3.670866	0	0
91.0	3.670866	1	1
92.0	3.670866	0	0
93.0	3.670866	1	1
94.0	3.670866	0	0
95.0	3.670866	1	1
96.0	3.670866	0	0
97.0	3.670866	0	0
98.0	3.670866	0	0
99.0	3.670866	0	0
100.0	3.670866	0	0
104.0	0	1	1
109.0	0	1	1
134.0	0	1	1
318.0	0	1	1