## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2015-06-30/DE_Bad_Bro_1_2015-06-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2015-06-30/DE_Bad_Bro_1_2015-06-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2015-06-30/DE_Bad_Bro_1_2015-06-30.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 09:15:41 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	12333256	35597046	0	0	5384884	5708903	0	0.201164	98766873

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	24628173	24628173
2.0	1.697387	4030160	4030160
3.0	2.183736	615517	615517
4.0	2.522909	94565	94565
5.0	2.759444	16427	16427
6.0	2.9244	3735	3735
7.0	3.039438	1263	1263
8.0	3.119665	651	651
9.0	3.175614	403	403
10.0	3.214632	308	308
11.0	3.241842	228	228
12.0	3.260818	197	197
13.0	3.274052	158	158
14.0	3.283281	123	123
15.0	3.289718	137	137
16.0	3.294206	111	111
17.0	3.297336	86	86
18.0	3.299519	81	81
19.0	3.301042	68	68
20.0	3.302104	56	56
21.0	3.302844	43	43
22.0	3.30336	58	58
23.0	3.30372	47	47
24.0	3.303972	42	42
25.0	3.304147	34	34
26.0	3.304269	29	29
27.0	3.304354	26	26
28.0	3.304413	23	23
29.0	3.304455	34	34
30.0	3.304484	31	31
31.0	3.304504	17	17
32.0	3.304518	18	18
33.0	3.304528	23	23
34.0	3.304535	13	13
35.0	3.304539	14	14
36.0	3.304543	19	19
37.0	3.304545	18	18
38.0	3.304547	7	7
39.0	3.304548	9	9
40.0	3.304549	9	9
41.0	3.304549	16	16
42.0	3.304549	7	7
43.0	3.30455	9	9
44.0	3.30455	17	17
45.0	3.30455	12	12
46.0	3.30455	8	8
47.0	3.30455	8	8
48.0	3.30455	10	10
49.0	3.30455	3	3
50.0	3.30455	8	8
51.0	3.30455	3	3
52.0	3.30455	9	9
53.0	3.30455	6	6
54.0	3.30455	4	4
55.0	3.30455	14	14
56.0	3.30455	12	12
57.0	3.30455	6	6
58.0	3.30455	4	4
59.0	3.30455	6	6
60.0	3.30455	7	7
61.0	3.30455	6	6
62.0	3.30455	2	2
63.0	3.30455	3	3
64.0	3.30455	7	7
65.0	3.30455	0	0
66.0	3.30455	7	7
67.0	3.30455	4	4
68.0	3.30455	2	2
69.0	3.30455	5	5
70.0	3.30455	5	5
71.0	3.30455	3	3
72.0	3.30455	4	4
73.0	3.30455	5	5
74.0	3.30455	2	2
75.0	3.30455	2	2
76.0	3.30455	4	4
77.0	3.30455	2	2
78.0	3.30455	4	4
79.0	3.30455	4	4
80.0	3.30455	3	3
81.0	3.30455	1	1
82.0	3.30455	3	3
83.0	3.30455	2	2
84.0	3.30455	3	3
85.0	3.30455	2	2
86.0	3.30455	3	3
87.0	3.30455	0	0
88.0	3.30455	3	3
89.0	3.30455	2	2
90.0	3.30455	1	1
91.0	3.30455	2	2
92.0	3.30455	0	0
93.0	3.30455	1	1
94.0	3.30455	2	2
95.0	3.30455	1	1
96.0	3.30455	2	2
97.0	3.30455	1	1
98.0	3.30455	0	0
99.0	3.30455	4	4
100.0	3.30455	4	4
101.0	0	2	2
102.0	0	2	2
103.0	0	5	5
104.0	0	1	1
107.0	0	4	4
109.0	0	1	1
111.0	0	2	2
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
117.0	0	1	1
118.0	0	1	1
119.0	0	1	1
120.0	0	3	3
122.0	0	4	4
124.0	0	1	1
128.0	0	2	2
129.0	0	2	2
130.0	0	2	2
132.0	0	1	1
133.0	0	1	1
134.0	0	2	2
137.0	0	2	2
138.0	0	1	1
140.0	0	1	1
141.0	0	1	1
145.0	0	1	1
147.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	1	1
158.0	0	1	1
163.0	0	1	1
170.0	0	1	1
183.0	0	1	1
186.0	0	1	1
190.0	0	1	1
193.0	0	1	1
195.0	0	1	1
199.0	0	1	1
210.0	0	1	1
214.0	0	1	1
216.0	0	1	1
221.0	0	1	1
228.0	0	1	1
230.0	0	1	1
249.0	0	1	1
267.0	0	1	1
291.0	0	1	1
299.0	0	1	1
302.0	0	1	1
321.0	0	1	1
379.0	0	1	1
385.0	0	1	1
428.0	0	1	1
449.0	0	1	1
481.0	0	1	1
692.0	0	1	1
986.0	0	1	1