## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CA_Ont_Sud_1_2015-09-30/CA_Ont_Sud_1_2015-09-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CA_Ont_Sud_1_2015-09-30/CA_Ont_Sud_1_2015-09-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CA_Ont_Sud_1_2015-09-30/CA_Ont_Sud_1_2015-09-30.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 09:10:29 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	1502685	38520721	0	0	621445	2269136	0	0.065692	313992335

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	33353261	33353261
2.0	1.884546	1949655	1949655
3.0	2.666968	108820	108820
4.0	3.359057	8175	8175
5.0	3.971241	1625	1625
6.0	4.512747	836	836
7.0	4.991733	559	559
8.0	5.415419	367	367
9.0	5.790189	285	285
10.0	6.12169	239	239
11.0	6.414918	178	178
12.0	6.674292	148	148
13.0	6.90372	126	126
14.0	7.10666	117	117
15.0	7.286169	114	114
16.0	7.444954	99	99
17.0	7.585406	84	84
18.0	7.709643	69	69
19.0	7.819536	77	77
20.0	7.916741	62	62
21.0	8.002724	43	43
22.0	8.07878	52	52
23.0	8.146055	30	30
24.0	8.205562	40	40
25.0	8.258199	38	38
26.0	8.30476	33	33
27.0	8.345944	39	39
28.0	8.382374	34	34
29.0	8.414597	32	32
30.0	8.443101	26	26
31.0	8.468313	20	20
32.0	8.490615	17	17
33.0	8.510342	20	20
34.0	8.527791	20	20
35.0	8.543226	14	14
36.0	8.556879	14	14
37.0	8.568955	15	15
38.0	8.579637	18	18
39.0	8.589086	18	18
40.0	8.597444	14	14
41.0	8.604837	9	9
42.0	8.611377	10	10
43.0	8.617161	14	14
44.0	8.622278	8	8
45.0	8.626804	8	8
46.0	8.630807	6	6
47.0	8.634348	6	6
48.0	8.637481	11	11
49.0	8.640251	8	8
50.0	8.642702	12	12
51.0	8.64487	12	12
52.0	8.646787	7	7
53.0	8.648484	4	4
54.0	8.649984	5	5
55.0	8.651311	4	4
56.0	8.652485	8	8
57.0	8.653523	4	4
58.0	8.654442	5	5
59.0	8.655254	7	7
60.0	8.655973	2	2
61.0	8.656609	5	5
62.0	8.657171	2	2
63.0	8.657668	2	2
64.0	8.658108	4	4
65.0	8.658497	5	5
66.0	8.658842	4	4
67.0	8.659146	3	3
68.0	8.659415	2	2
69.0	8.659654	6	6
70.0	8.659864	3	3
71.0	8.660051	3	3
72.0	8.660216	1	1
73.0	8.660361	1	1
74.0	8.66049	2	2
75.0	8.660605	1	1
76.0	8.660705	1	1
77.0	8.660795	2	2
78.0	8.660874	5	5
79.0	8.660944	6	6
80.0	8.661005	2	2
81.0	8.66106	1	1
82.0	8.661108	2	2
83.0	8.661151	3	3
84.0	8.661189	2	2
85.0	8.661222	2	2
86.0	8.661252	5	5
87.0	8.661278	2	2
88.0	8.661301	4	4
89.0	8.661322	0	0
90.0	8.66134	2	2
91.0	8.661356	4	4
92.0	8.66137	2	2
93.0	8.661383	0	0
94.0	8.661394	2	2
95.0	8.661404	2	2
96.0	8.661412	4	4
97.0	8.66142	2	2
98.0	8.661427	2	2
99.0	8.661433	1	1
100.0	8.661438	2	2
103.0	0	1	1
104.0	0	3	3
105.0	0	5	5
106.0	0	1	1
107.0	0	1	1
109.0	0	7	7
111.0	0	2	2
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
118.0	0	2	2
120.0	0	1	1
122.0	0	2	2
124.0	0	1	1
127.0	0	1	1
128.0	0	2	2
130.0	0	2	2
133.0	0	1	1
134.0	0	1	1
137.0	0	1	1
139.0	0	1	1
140.0	0	1	1
141.0	0	1	1
142.0	0	3	3
143.0	0	3	3
148.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	1	1
155.0	0	1	1
158.0	0	1	1
159.0	0	3	3
160.0	0	2	2
161.0	0	4	4
164.0	0	1	1
166.0	0	1	1
167.0	0	1	1
169.0	0	1	1
172.0	0	1	1
175.0	0	1	1
176.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
184.0	0	1	1
190.0	0	1	1
197.0	0	1	1
198.0	0	1	1
202.0	0	1	1
218.0	0	1	1
238.0	0	1	1
260.0	0	1	1
331.0	0	1	1