## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-20/UA_Kie_Cho_1_2015-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-20/UA_Kie_Cho_1_2015-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-20/UA_Kie_Cho_1_2015-08-20.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 08:38:32 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	13110612	23746261	0	0	5197791	5782189	0	0.276589	40473857

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	13227924	13227924
2.0	1.556156	3383997	3383997
3.0	1.865466	811063	811063
4.0	2.03749	181483	181483
5.0	2.133163	38514	38514
6.0	2.186372	8078	8078
7.0	2.215964	1815	1815
8.0	2.232422	509	509
9.0	2.241575	226	226
10.0	2.246666	147	147
11.0	2.249497	107	107
12.0	2.251072	99	99
13.0	2.251947	69	69
14.0	2.252434	65	65
15.0	2.252705	57	57
16.0	2.252856	43	43
17.0	2.25294	41	41
18.0	2.252986	39	39
19.0	2.253012	47	47
20.0	2.253027	31	31
21.0	2.253035	20	20
22.0	2.253039	20	20
23.0	2.253042	23	23
24.0	2.253043	19	19
25.0	2.253044	14	14
26.0	2.253044	8	8
27.0	2.253044	18	18
28.0	2.253045	19	19
29.0	2.253045	10	10
30.0	2.253045	9	9
31.0	2.253045	12	12
32.0	2.253045	8	8
33.0	2.253045	10	10
34.0	2.253045	8	8
35.0	2.253045	11	11
36.0	2.253045	3	3
37.0	2.253045	6	6
38.0	2.253045	2	2
39.0	2.253045	10	10
40.0	2.253045	6	6
41.0	2.253045	1	1
42.0	2.253045	4	4
43.0	2.253045	4	4
44.0	2.253045	5	5
45.0	2.253045	3	3
46.0	2.253045	7	7
47.0	2.253045	2	2
48.0	2.253045	5	5
49.0	2.253045	6	6
50.0	2.253045	0	0
51.0	2.253045	4	4
52.0	2.253045	1	1
53.0	2.253045	5	5
54.0	2.253045	2	2
55.0	2.253045	2	2
56.0	2.253045	2	2
57.0	2.253045	0	0
58.0	2.253045	1	1
59.0	2.253045	2	2
60.0	2.253045	2	2
61.0	2.253045	0	0
62.0	2.253045	1	1
63.0	2.253045	2	2
64.0	2.253045	0	0
65.0	2.253045	2	2
66.0	2.253045	1	1
67.0	2.253045	0	0
68.0	2.253045	0	0
69.0	2.253045	2	2
70.0	2.253045	1	1
71.0	2.253045	0	0
72.0	2.253045	1	1
73.0	2.253045	1	1
74.0	2.253045	1	1
75.0	2.253045	1	1
76.0	2.253045	0	0
77.0	2.253045	0	0
78.0	2.253045	0	0
79.0	2.253045	1	1
80.0	2.253045	0	0
81.0	2.253045	0	0
82.0	2.253045	1	1
83.0	2.253045	0	0
84.0	2.253045	1	1
85.0	2.253045	1	1
86.0	2.253045	0	0
87.0	2.253045	2	2
88.0	2.253045	0	0
89.0	2.253045	0	0
90.0	2.253045	0	0
91.0	2.253045	0	0
92.0	2.253045	0	0
93.0	2.253045	1	1
94.0	2.253045	0	0
95.0	2.253045	0	0
96.0	2.253045	0	0
97.0	2.253045	0	0
98.0	2.253045	0	0
99.0	2.253045	0	0
100.0	2.253045	1	1
109.0	0	1	1
111.0	0	1	1
127.0	0	1	1
154.0	0	1	1
156.0	0	1	1
174.0	0	1	1