## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-08-27/UA_Ode_Ode_1_2015-08-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-08-27/UA_Ode_Ode_1_2015-08-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-08-27/UA_Ode_Ode_1_2015-08-27.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 17:28:04 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	5184100	32490488	0	0	1999741	2927176	0	0.111937	169314639

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26541189	26541189
2.0	1.825394	2412421	2412421
3.0	2.50667	190469	190469
4.0	3.068991	15499	15499
5.0	3.533127	1885	1885
6.0	3.916223	652	652
7.0	4.232428	481	481
8.0	4.493422	354	354
9.0	4.708844	265	265
10.0	4.886653	213	213
11.0	5.033415	228	228
12.0	5.154552	162	162
13.0	5.254537	153	153
14.0	5.337065	142	142
15.0	5.405183	123	123
16.0	5.461407	110	110
17.0	5.507813	96	96
18.0	5.546117	101	101
19.0	5.577733	83	83
20.0	5.603829	59	59
21.0	5.625368	54	54
22.0	5.643146	46	46
23.0	5.657821	46	46
24.0	5.669932	43	43
25.0	5.67993	42	42
26.0	5.688181	43	43
27.0	5.694992	36	36
28.0	5.700613	27	27
29.0	5.705254	33	33
30.0	5.709083	41	41
31.0	5.712244	34	34
32.0	5.714854	19	19
33.0	5.717007	26	26
34.0	5.718785	21	21
35.0	5.720252	22	22
36.0	5.721463	21	21
37.0	5.722463	22	22
38.0	5.723288	25	25
39.0	5.723969	23	23
40.0	5.724531	13	13
41.0	5.724995	17	17
42.0	5.725378	19	19
43.0	5.725694	11	11
44.0	5.725955	15	15
45.0	5.72617	18	18
46.0	5.726348	13	13
47.0	5.726494	12	12
48.0	5.726615	11	11
49.0	5.726715	12	12
50.0	5.726798	12	12
51.0	5.726866	13	13
52.0	5.726922	9	9
53.0	5.726968	6	6
54.0	5.727007	9	9
55.0	5.727038	8	8
56.0	5.727064	13	13
57.0	5.727086	6	6
58.0	5.727104	5	5
59.0	5.727118	10	10
60.0	5.727131	8	8
61.0	5.727141	7	7
62.0	5.727149	7	7
63.0	5.727156	7	7
64.0	5.727161	9	9
65.0	5.727166	6	6
66.0	5.72717	3	3
67.0	5.727173	4	4
68.0	5.727175	8	8
69.0	5.727178	7	7
70.0	5.727179	7	7
71.0	5.727181	7	7
72.0	5.727182	1	1
73.0	5.727183	3	3
74.0	5.727184	3	3
75.0	5.727185	3	3
76.0	5.727185	2	2
77.0	5.727186	1	1
78.0	5.727186	4	4
79.0	5.727186	3	3
80.0	5.727187	2	2
81.0	5.727187	3	3
82.0	5.727187	3	3
83.0	5.727187	2	2
84.0	5.727187	2	2
85.0	5.727187	6	6
86.0	5.727187	3	3
87.0	5.727187	3	3
88.0	5.727188	2	2
89.0	5.727188	3	3
90.0	5.727188	5	5
91.0	5.727188	4	4
92.0	5.727188	3	3
93.0	5.727188	2	2
94.0	5.727188	1	1
95.0	5.727188	4	4
96.0	5.727188	1	1
97.0	5.727188	1	1
98.0	5.727188	2	2
99.0	5.727188	0	0
100.0	5.727188	1	1
102.0	0	1	1
103.0	0	2	2
104.0	0	1	1
105.0	0	1	1
106.0	0	1	1
109.0	0	1	1
111.0	0	3	3
112.0	0	2	2
113.0	0	2	2
114.0	0	1	1
115.0	0	1	1
118.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	2	2
124.0	0	3	3
125.0	0	2	2
126.0	0	2	2
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
135.0	0	2	2
136.0	0	1	1
138.0	0	1	1
139.0	0	1	1
141.0	0	2	2
142.0	0	1	1
143.0	0	1	1
144.0	0	2	2
147.0	0	1	1
148.0	0	3	3
152.0	0	1	1
154.0	0	1	1
157.0	0	1	1
162.0	0	1	1
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
174.0	0	1	1
179.0	0	2	2
180.0	0	1	1
192.0	0	1	1
195.0	0	1	1
196.0	0	1	1
199.0	0	1	1
200.0	0	1	1
212.0	0	1	1
252.0	0	1	1
257.0	0	1	1
273.0	0	1	1
347.0	0	1	1
361.0	0	1	1
435.0	0	1	1