## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-10-22/US_Kan_Top_1_2014-10-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-10-22/US_Kan_Top_1_2014-10-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-10-22/US_Kan_Top_1_2014-10-22.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 18:51:17 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	1366097	37738617	0	0	554027	12058425	0	0.321054	45658681

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	16035096	16035096
2.0	1.437562	6113700	6113700
3.0	1.629022	1882424	1882424
4.0	1.712798	486321	486321
5.0	1.749455	112310	112310
6.0	1.765494	24475	24475
7.0	1.772513	5774	5774
8.0	1.775584	1878	1878
9.0	1.776927	860	860
10.0	1.777515	537	537
11.0	1.777773	405	405
12.0	1.777885	303	303
13.0	1.777934	197	197
14.0	1.777956	173	173
15.0	1.777965	156	156
16.0	1.77797	132	132
17.0	1.777971	110	110
18.0	1.777972	91	91
19.0	1.777972	74	74
20.0	1.777973	70	70
21.0	1.777973	53	53
22.0	1.777973	69	69
23.0	1.777973	67	67
24.0	1.777973	40	40
25.0	1.777973	50	50
26.0	1.777973	40	40
27.0	1.777973	44	44
28.0	1.777973	23	23
29.0	1.777973	31	31
30.0	1.777973	38	38
31.0	1.777973	27	27
32.0	1.777973	17	17
33.0	1.777973	28	28
34.0	1.777973	24	24
35.0	1.777973	23	23
36.0	1.777973	27	27
37.0	1.777973	22	22
38.0	1.777973	21	21
39.0	1.777973	17	17
40.0	1.777973	10	10
41.0	1.777973	5	5
42.0	1.777973	10	10
43.0	1.777973	13	13
44.0	1.777973	12	12
45.0	1.777973	17	17
46.0	1.777973	14	14
47.0	1.777973	9	9
48.0	1.777973	7	7
49.0	1.777973	5	5
50.0	1.777973	8	8
51.0	1.777973	11	11
52.0	1.777973	6	6
53.0	1.777973	8	8
54.0	1.777973	6	6
55.0	1.777973	5	5
56.0	1.777973	4	4
57.0	1.777973	11	11
58.0	1.777973	7	7
59.0	1.777973	3	3
60.0	1.777973	2	2
61.0	1.777973	6	6
62.0	1.777973	2	2
63.0	1.777973	4	4
64.0	1.777973	6	6
65.0	1.777973	5	5
66.0	1.777973	5	5
67.0	1.777973	1	1
68.0	1.777973	5	5
69.0	1.777973	4	4
70.0	1.777973	4	4
71.0	1.777973	4	4
72.0	1.777973	3	3
73.0	1.777973	4	4
74.0	1.777973	1	1
75.0	1.777973	4	4
76.0	1.777973	2	2
77.0	1.777973	3	3
78.0	1.777973	4	4
79.0	1.777973	1	1
80.0	1.777973	5	5
81.0	1.777973	2	2
82.0	1.777973	4	4
83.0	1.777973	4	4
84.0	1.777973	2	2
85.0	1.777973	0	0
86.0	1.777973	2	2
87.0	1.777973	2	2
88.0	1.777973	3	3
89.0	1.777973	1	1
90.0	1.777973	2	2
91.0	1.777973	1	1
92.0	1.777973	3	3
93.0	1.777973	3	3
94.0	1.777973	2	2
95.0	1.777973	0	0
96.0	1.777973	1	1
97.0	1.777973	0	0
98.0	1.777973	3	3
99.0	1.777973	1	1
100.0	1.777973	0	0
102.0	0	4	4
103.0	0	2	2
106.0	0	1	1
107.0	0	2	2
108.0	0	2	2
109.0	0	2	2
110.0	0	2	2
111.0	0	4	4
112.0	0	1	1
113.0	0	3	3
114.0	0	4	4
115.0	0	2	2
118.0	0	2	2
120.0	0	1	1
123.0	0	2	2
124.0	0	3	3
126.0	0	1	1
130.0	0	1	1
132.0	0	1	1
136.0	0	2	2
138.0	0	2	2
139.0	0	1	1
142.0	0	1	1
143.0	0	1	1
146.0	0	1	1
147.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	4	4
153.0	0	2	2
155.0	0	2	2
157.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
164.0	0	1	1
166.0	0	2	2
169.0	0	1	1
171.0	0	2	2
173.0	0	2	2
174.0	0	1	1
176.0	0	1	1
177.0	0	2	2
178.0	0	2	2
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
186.0	0	1	1
188.0	0	1	1
192.0	0	1	1
194.0	0	1	1
197.0	0	2	2
204.0	0	1	1
205.0	0	1	1
207.0	0	1	1
208.0	0	2	2
209.0	0	1	1
211.0	0	1	1
212.0	0	1	1
217.0	0	1	1
218.0	0	2	2
219.0	0	1	1
232.0	0	1	1
242.0	0	2	2
253.0	0	1	1
256.0	0	1	1
265.0	0	1	1
270.0	0	1	1
278.0	0	1	1
284.0	0	1	1
307.0	0	1	1
323.0	0	1	1
368.0	0	1	1
380.0	0	1	1
387.0	0	1	1
438.0	0	1	1
448.0	0	1	1
449.0	0	1	1
458.0	0	1	1
464.0	0	1	1
490.0	0	1	1
515.0	0	1	1
554.0	0	1	1
635.0	0	1	1
792.0	0	1	1
807.0	0	1	1
809.0	0	1	1
820.0	0	1	1
847.0	0	1	1
968.0	0	1	1
1023.0	0	1	1
1171.0	0	1	1
1482.0	0	1	1
1758.0	0	1	1