## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-09-01/DE_Bay_Mun_1_2015-09-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-09-01/DE_Bay_Mun_1_2015-09-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-09-01/DE_Bay_Mun_1_2015-09-01.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 08:45:32 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	5917085	34913060	0	0	2558107	4503033	0	0.152676	123437828

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26216225	26216225
2.0	1.753641	3452167	3452167
3.0	2.321616	415455	415455
4.0	2.749665	49647	49647
5.0	3.07226	6535	6535
6.0	3.315381	1114	1114
7.0	3.498607	450	450
8.0	3.636693	274	274
9.0	3.740761	197	197
10.0	3.819191	202	202
11.0	3.878298	133	133
12.0	3.922844	103	103
13.0	3.956416	108	108
14.0	3.981717	84	84
15.0	4.000785	86	86
16.0	4.015155	71	71
17.0	4.025986	67	67
18.0	4.034148	52	52
19.0	4.040299	50	50
20.0	4.044935	48	48
21.0	4.048428	43	43
22.0	4.051061	27	27
23.0	4.053046	32	32
24.0	4.054541	31	31
25.0	4.055668	40	40
26.0	4.056518	30	30
27.0	4.057158	20	20
28.0	4.05764	23	23
29.0	4.058004	27	27
30.0	4.058278	20	20
31.0	4.058484	11	11
32.0	4.05864	12	12
33.0	4.058757	18	18
34.0	4.058846	9	9
35.0	4.058912	5	5
36.0	4.058962	17	17
37.0	4.059	10	10
38.0	4.059029	4	4
39.0	4.05905	15	15
40.0	4.059066	9	9
41.0	4.059079	9	9
42.0	4.059088	5	5
43.0	4.059095	4	4
44.0	4.0591	7	7
45.0	4.059104	3	3
46.0	4.059107	3	3
47.0	4.059109	2	2
48.0	4.059111	3	3
49.0	4.059112	6	6
50.0	4.059113	2	2
51.0	4.059114	3	3
52.0	4.059114	1	1
53.0	4.059115	4	4
54.0	4.059115	4	4
55.0	4.059115	1	1
56.0	4.059115	3	3
57.0	4.059116	2	2
58.0	4.059116	4	4
59.0	4.059116	2	2
60.0	4.059116	6	6
61.0	4.059116	2	2
62.0	4.059116	4	4
63.0	4.059116	4	4
64.0	4.059116	3	3
65.0	4.059116	0	0
66.0	4.059116	5	5
67.0	4.059116	3	3
68.0	4.059116	3	3
69.0	4.059116	2	2
70.0	4.059116	3	3
71.0	4.059116	1	1
72.0	4.059116	2	2
73.0	4.059116	1	1
74.0	4.059116	3	3
75.0	4.059116	2	2
76.0	4.059116	3	3
77.0	4.059116	0	0
78.0	4.059116	0	0
79.0	4.059116	1	1
80.0	4.059116	0	0
81.0	4.059116	1	1
82.0	4.059116	2	2
83.0	4.059116	0	0
84.0	4.059116	2	2
85.0	4.059116	0	0
86.0	4.059116	2	2
87.0	4.059116	0	0
88.0	4.059116	0	0
89.0	4.059116	0	0
90.0	4.059116	0	0
91.0	4.059116	3	3
92.0	4.059116	2	2
93.0	4.059116	0	0
94.0	4.059116	0	0
95.0	4.059116	1	1
96.0	4.059116	0	0
97.0	4.059116	0	0
98.0	4.059116	0	0
99.0	4.059116	0	0
100.0	4.059116	1	1
106.0	0	1	1
108.0	0	1	1
109.0	0	1	1
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
136.0	0	1	1
145.0	0	1	1
147.0	0	2	2
151.0	0	1	1
195.0	0	1	1
414.0	0	1	1