## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-06-28/ES_Ler_Gim_1_2015-06-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-06-28/ES_Ler_Gim_1_2015-06-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-06-28/ES_Ler_Gim_1_2015-06-28.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 08:54:35 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	9085670	29743509	0	0	3776750	2954528	0	0.141249	139627379

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23817891	23817891
2.0	1.808139	2414432	2414432
3.0	2.461229	219602	219602
4.0	2.989016	20476	20476
5.0	3.415542	2390	2390
6.0	3.760234	663	663
7.0	4.038794	336	336
8.0	4.263909	201	201
9.0	4.445833	151	151
10.0	4.592853	106	106
11.0	4.711666	102	102
12.0	4.807683	73	73
13.0	4.885279	57	57
14.0	4.947987	68	68
15.0	4.998663	52	52
16.0	5.039617	42	42
17.0	5.072714	32	32
18.0	5.09946	24	24
19.0	5.121075	25	25
20.0	5.138543	17	17
21.0	5.15266	30	30
22.0	5.164068	21	21
23.0	5.173287	21	21
24.0	5.180737	14	14
25.0	5.186758	25	25
26.0	5.191624	13	13
27.0	5.195557	11	11
28.0	5.198734	18	18
29.0	5.201303	13	13
30.0	5.203378	13	13
31.0	5.205055	11	11
32.0	5.206411	8	8
33.0	5.207506	6	6
34.0	5.208391	4	4
35.0	5.209107	5	5
36.0	5.209685	8	8
37.0	5.210152	5	5
38.0	5.210529	6	6
39.0	5.210835	6	6
40.0	5.211081	1	1
41.0	5.21128	6	6
42.0	5.211441	1	1
43.0	5.211572	5	5
44.0	5.211677	8	8
45.0	5.211762	6	6
46.0	5.211831	4	4
47.0	5.211886	4	4
48.0	5.211931	4	4
49.0	5.211967	2	2
50.0	5.211996	1	1
51.0	5.21202	2	2
52.0	5.212039	2	2
53.0	5.212055	3	3
54.0	5.212067	2	2
55.0	5.212077	5	5
56.0	5.212085	1	1
57.0	5.212092	6	6
58.0	5.212097	2	2
59.0	5.212102	1	1
60.0	5.212105	3	3
61.0	5.212108	2	2
62.0	5.21211	1	1
63.0	5.212112	2	2
64.0	5.212114	1	1
65.0	5.212115	1	1
66.0	5.212116	1	1
67.0	5.212117	2	2
68.0	5.212117	0	0
69.0	5.212118	1	1
70.0	5.212118	0	0
71.0	5.212118	0	0
72.0	5.212119	0	0
73.0	5.212119	1	1
74.0	5.212119	1	1
75.0	5.212119	0	0
76.0	5.212119	0	0
77.0	5.212119	1	1
78.0	5.21212	0	0
79.0	5.21212	1	1
80.0	5.21212	1	1
81.0	5.21212	1	1
82.0	5.21212	2	2
83.0	5.21212	1	1
84.0	5.21212	1	1
85.0	5.21212	0	0
86.0	5.21212	0	0
87.0	5.21212	2	2
88.0	5.21212	0	0
89.0	5.21212	0	0
90.0	5.21212	1	1
91.0	5.21212	1	1
92.0	5.21212	1	1
93.0	5.21212	0	0
94.0	5.21212	0	0
95.0	5.21212	0	0
96.0	5.21212	0	0
97.0	5.21212	0	0
98.0	5.21212	0	0
99.0	5.21212	0	0
100.0	5.21212	0	0
102.0	0	1	1
104.0	0	1	1
105.0	0	2	2
107.0	0	1	1
108.0	0	1	1
109.0	0	1	1
112.0	0	2	2
114.0	0	1	1
118.0	0	1	1
121.0	0	1	1
131.0	0	2	2
136.0	0	1	1
144.0	0	1	1
233.0	0	1	1
260.0	0	1	1
361.0	0	1	1
391.0	0	1	1