## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-10-10/IT_Tre_San_1_2015-10-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-10-10/IT_Tre_San_1_2015-10-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-10-10/IT_Tre_San_1_2015-10-10.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 08:55:21 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	6901688	32264485	0	0	2156503	3011289	0	0.114504	161918061

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25908484	25908484
2.0	1.819333	2474889	2474889
3.0	2.49064	203236	203236
4.0	3.040665	17593	17593
5.0	3.491318	2508	2508
6.0	3.860553	970	970
7.0	4.16308	573	573
8.0	4.41095	431	431
9.0	4.614039	316	316
10.0	4.780436	281	281
11.0	4.91677	214	214
12.0	5.028474	177	177
13.0	5.119996	138	138
14.0	5.194984	117	117
15.0	5.256423	86	86
16.0	5.306763	91	91
17.0	5.348008	86	86
18.0	5.381801	78	78
19.0	5.409489	72	72
20.0	5.432175	64	64
21.0	5.450762	64	64
22.0	5.465991	43	43
23.0	5.478468	46	46
24.0	5.488692	39	39
25.0	5.497068	35	35
26.0	5.503931	33	33
27.0	5.509554	29	29
28.0	5.514162	24	24
29.0	5.517936	22	22
30.0	5.521029	14	14
31.0	5.523563	24	24
32.0	5.52564	18	18
33.0	5.527341	28	28
34.0	5.528734	9	9
35.0	5.529876	16	16
36.0	5.530812	14	14
37.0	5.531579	15	15
38.0	5.532207	15	15
39.0	5.532721	11	11
40.0	5.533143	6	6
41.0	5.533489	14	14
42.0	5.533772	15	15
43.0	5.534004	11	11
44.0	5.534194	10	10
45.0	5.534349	6	6
46.0	5.534477	6	6
47.0	5.534581	13	13
48.0	5.534667	2	2
49.0	5.534737	11	11
50.0	5.534795	6	6
51.0	5.534842	7	7
52.0	5.53488	10	10
53.0	5.534912	6	6
54.0	5.534938	5	5
55.0	5.534959	5	5
56.0	5.534977	4	4
57.0	5.534991	3	3
58.0	5.535002	4	4
59.0	5.535012	7	7
60.0	5.53502	8	8
61.0	5.535026	5	5
62.0	5.535032	6	6
63.0	5.535036	8	8
64.0	5.535039	5	5
65.0	5.535042	5	5
66.0	5.535045	2	2
67.0	5.535047	6	6
68.0	5.535048	2	2
69.0	5.53505	2	2
70.0	5.535051	2	2
71.0	5.535051	5	5
72.0	5.535052	1	1
73.0	5.535053	1	1
74.0	5.535053	2	2
75.0	5.535054	3	3
76.0	5.535054	2	2
77.0	5.535054	1	1
78.0	5.535054	0	0
79.0	5.535055	1	1
80.0	5.535055	1	1
81.0	5.535055	0	0
82.0	5.535055	2	2
83.0	5.535055	3	3
84.0	5.535055	0	0
85.0	5.535055	2	2
86.0	5.535055	1	1
87.0	5.535055	1	1
88.0	5.535055	2	2
89.0	5.535055	1	1
90.0	5.535055	2	2
91.0	5.535055	0	0
92.0	5.535055	2	2
93.0	5.535055	0	0
94.0	5.535055	0	0
95.0	5.535055	1	1
96.0	5.535055	1	1
97.0	5.535055	1	1
98.0	5.535055	2	2
99.0	5.535055	1	1
100.0	5.535055	0	0
101.0	0	1	1
102.0	0	1	1
103.0	0	2	2
105.0	0	1	1
107.0	0	1	1
108.0	0	1	1
110.0	0	4	4
112.0	0	1	1
119.0	0	1	1
121.0	0	3	3
122.0	0	1	1
123.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
135.0	0	2	2
137.0	0	1	1
140.0	0	1	1
142.0	0	2	2
146.0	0	1	1
159.0	0	1	1
161.0	0	2	2
163.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
195.0	0	1	1
200.0	0	1	1
202.0	0	1	1
299.0	0	1	1
318.0	0	1	1
359.0	0	1	1
479.0	0	1	1
519.0	0	1	1
685.0	0	1	1
1143.0	0	1	1