## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-06-01/TR_Ank_Yes_1_2015-06-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-06-01/TR_Ank_Yes_1_2015-06-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-06-01/TR_Ank_Yes_1_2015-06-01.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 08:48:31 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	11547504	29403177	0	0	7480251	18261456	0	0.625455	12253944

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	3354823	3354823
2.0	1.090764	2630159	2630159
3.0	1.099003	1971316	1971316
4.0	1.09975	1304500	1304500
5.0	1.099818	776525	776525
6.0	1.099824	417550	417550
7.0	1.099825	209426	209426
8.0	1.099825	97546	97546
9.0	1.099825	42497	42497
10.0	1.099825	17883	17883
11.0	1.099825	7167	7167
12.0	1.099825	2814	2814
13.0	1.099825	1108	1108
14.0	1.099825	455	455
15.0	1.099825	200	200
16.0	1.099825	86	86
17.0	1.099825	61	61
18.0	1.099825	38	38
19.0	1.099825	27	27
20.0	1.099825	29	29
21.0	1.099825	25	25
22.0	1.099825	18	18
23.0	1.099825	18	18
24.0	1.099825	12	12
25.0	1.099825	10	10
26.0	1.099825	18	18
27.0	1.099825	10	10
28.0	1.099825	12	12
29.0	1.099825	7	7
30.0	1.099825	17	17
31.0	1.099825	5	5
32.0	1.099825	14	14
33.0	1.099825	7	7
34.0	1.099825	6	6
35.0	1.099825	6	6
36.0	1.099825	6	6
37.0	1.099825	4	4
38.0	1.099825	10	10
39.0	1.099825	5	5
40.0	1.099825	5	5
41.0	1.099825	3	3
42.0	1.099825	4	4
43.0	1.099825	5	5
44.0	1.099825	5	5
45.0	1.099825	2	2
46.0	1.099825	6	6
47.0	1.099825	2	2
48.0	1.099825	3	3
49.0	1.099825	4	4
50.0	1.099825	1	1
51.0	1.099825	4	4
52.0	1.099825	3	3
53.0	1.099825	1	1
54.0	1.099825	0	0
55.0	1.099825	2	2
56.0	1.099825	4	4
57.0	1.099825	1	1
58.0	1.099825	0	0
59.0	1.099825	5	5
60.0	1.099825	0	0
61.0	1.099825	1	1
62.0	1.099825	1	1
63.0	1.099825	0	0
64.0	1.099825	0	0
65.0	1.099825	0	0
66.0	1.099825	1	1
67.0	1.099825	0	0
68.0	1.099825	0	0
69.0	1.099825	1	1
70.0	1.099825	0	0
71.0	1.099825	3	3
72.0	1.099825	1	1
73.0	1.099825	1	1
74.0	1.099825	0	0
75.0	1.099825	0	0
76.0	1.099825	0	0
77.0	1.099825	0	0
78.0	1.099825	0	0
79.0	1.099825	1	1
80.0	1.099825	1	1
81.0	1.099825	1	1
82.0	1.099825	1	1
83.0	1.099825	1	1
84.0	1.099825	0	0
85.0	1.099825	0	0
86.0	1.099825	1	1
87.0	1.099825	1	1
88.0	1.099825	1	1
89.0	1.099825	0	0
90.0	1.099825	0	0
91.0	1.099825	0	0
92.0	1.099825	0	0
93.0	1.099825	0	0
94.0	1.099825	0	0
95.0	1.099825	0	0
96.0	1.099825	1	1
97.0	1.099825	1	1
98.0	1.099825	0	0
99.0	1.099825	0	0
100.0	1.099825	1	1
105.0	0	1	1
111.0	0	1	1
114.0	0	1	1
115.0	0	1	1
119.0	0	1	1
129.0	0	1	1
146.0	0	1	1
150.0	0	1	1
151.0	0	1	1
157.0	0	1	1
178.0	0	1	1
196.0	0	1	1
198.0	0	1	1
247.0	0	1	1
322.0	0	1	1