## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-06-25/DE_Bay_Mun_1_2016-06-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-06-25/DE_Bay_Mun_1_2016-06-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-06-25/DE_Bay_Mun_1_2016-06-25.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 08:55:37 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	28960150	12041219	0	0	6707686	975119	0	0.163226	70274874

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10048029	10048029
2.0	1.842531	695930	695930
3.0	2.55239	54949	54949
4.0	3.150468	6191	6191
5.0	3.654368	1713	1713
6.0	4.078919	943	943
7.0	4.436616	618	618
8.0	4.737988	489	489
9.0	4.991903	406	406
10.0	5.205834	299	299
11.0	5.386077	223	223
12.0	5.537938	232	232
13.0	5.665886	187	187
14.0	5.773685	197	197
15.0	5.86451	166	166
16.0	5.941033	153	153
17.0	6.005505	147	147
18.0	6.059826	124	124
19.0	6.105592	122	122
20.0	6.144152	99	99
21.0	6.17664	107	107
22.0	6.204012	95	95
23.0	6.227073	89	89
24.0	6.246504	67	67
25.0	6.262874	75	75
26.0	6.276667	79	79
27.0	6.288288	60	60
28.0	6.298079	63	63
29.0	6.306328	47	47
30.0	6.313278	43	43
31.0	6.319134	47	47
32.0	6.324067	45	45
33.0	6.328224	27	27
34.0	6.331726	37	37
35.0	6.334677	23	23
36.0	6.337163	17	17
37.0	6.339257	17	17
38.0	6.341022	30	30
39.0	6.342509	30	30
40.0	6.343762	23	23
41.0	6.344817	26	26
42.0	6.345706	27	27
43.0	6.346456	27	27
44.0	6.347087	29	29
45.0	6.347619	19	19
46.0	6.348067	23	23
47.0	6.348444	23	23
48.0	6.348762	14	14
49.0	6.34903	16	16
50.0	6.349256	19	19
51.0	6.349447	16	16
52.0	6.349607	15	15
53.0	6.349742	14	14
54.0	6.349856	19	19
55.0	6.349951	20	20
56.0	6.350032	21	21
57.0	6.3501	17	17
58.0	6.350158	18	18
59.0	6.350206	15	15
60.0	6.350247	17	17
61.0	6.350281	13	13
62.0	6.35031	14	14
63.0	6.350334	16	16
64.0	6.350355	15	15
65.0	6.350372	15	15
66.0	6.350387	15	15
67.0	6.350399	10	10
68.0	6.350409	9	9
69.0	6.350418	7	7
70.0	6.350425	18	18
71.0	6.350431	10	10
72.0	6.350437	9	9
73.0	6.350441	17	17
74.0	6.350445	10	10
75.0	6.350448	9	9
76.0	6.35045	9	9
77.0	6.350453	5	5
78.0	6.350454	10	10
79.0	6.350456	6	6
80.0	6.350457	9	9
81.0	6.350458	6	6
82.0	6.350459	7	7
83.0	6.35046	9	9
84.0	6.350461	13	13
85.0	6.350461	4	4
86.0	6.350462	10	10
87.0	6.350462	6	6
88.0	6.350463	4	4
89.0	6.350463	7	7
90.0	6.350463	5	5
91.0	6.350463	1	1
92.0	6.350463	4	4
93.0	6.350464	6	6
94.0	6.350464	3	3
95.0	6.350464	8	8
96.0	6.350464	5	5
97.0	6.350464	8	8
98.0	6.350464	4	4
99.0	6.350464	2	2
100.0	6.350464	1	1
101.0	0	5	5
102.0	0	2	2
103.0	0	5	5
104.0	0	4	4
105.0	0	5	5
106.0	0	2	2
107.0	0	3	3
108.0	0	5	5
109.0	0	3	3
110.0	0	4	4
112.0	0	2	2
113.0	0	1	1
114.0	0	2	2
115.0	0	2	2
116.0	0	3	3
117.0	0	2	2
118.0	0	2	2
119.0	0	2	2
120.0	0	2	2
121.0	0	2	2
122.0	0	1	1
123.0	0	1	1
124.0	0	2	2
125.0	0	2	2
126.0	0	1	1
127.0	0	2	2
130.0	0	1	1
132.0	0	1	1
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
137.0	0	1	1
138.0	0	2	2
139.0	0	1	1
140.0	0	1	1
142.0	0	3	3
143.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	6	6
151.0	0	4	4
153.0	0	2	2
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
160.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	3	3
165.0	0	2	2
167.0	0	1	1
170.0	0	1	1
171.0	0	1	1
174.0	0	1	1
176.0	0	2	2
178.0	0	1	1
180.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
196.0	0	1	1
197.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
212.0	0	1	1
218.0	0	1	1
222.0	0	1	1
239.0	0	1	1
243.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
255.0	0	2	2
257.0	0	1	1
258.0	0	1	1
260.0	0	2	2
261.0	0	1	1
264.0	0	2	2
267.0	0	1	1
270.0	0	1	1
272.0	0	1	1
280.0	0	1	1
291.0	0	1	1
295.0	0	1	1
308.0	0	1	1
312.0	0	1	1
340.0	0	1	1
346.0	0	1	1
349.0	0	1	1
355.0	0	1	1
365.0	0	1	1
369.0	0	1	1
411.0	0	1	1
416.0	0	1	1
516.0	0	1	1
517.0	0	1	1
534.0	0	1	1
602.0	0	1	1
624.0	0	1	1
780.0	0	1	1
979.0	0	1	1