## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-06-22/US_Kan_Top_1_2014-06-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-06-22/US_Kan_Top_1_2014-06-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Kan_Top_1_2014-06-22/US_Kan_Top_1_2014-06-22.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: Sat Jan 21 11:25:32 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	1266515	43288741	0	0	549987	12424137	0	0.289129	60163083

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20324120	20324120
2.0	1.486984	6810189	6810189
3.0	1.724138	1844216	1844216
4.0	1.839628	428019	428019
5.0	1.89587	91538	91538
6.0	1.923259	20394	20394
7.0	1.936597	5745	5745
8.0	1.943092	2549	2549
9.0	1.946256	1506	1506
10.0	1.947796	996	996
11.0	1.948546	711	711
12.0	1.948911	535	535
13.0	1.949089	429	429
14.0	1.949176	336	336
15.0	1.949218	275	275
16.0	1.949239	216	216
17.0	1.949249	170	170
18.0	1.949254	144	144
19.0	1.949256	126	126
20.0	1.949257	100	100
21.0	1.949258	92	92
22.0	1.949258	91	91
23.0	1.949258	75	75
24.0	1.949258	76	76
25.0	1.949258	61	61
26.0	1.949258	53	53
27.0	1.949258	53	53
28.0	1.949258	55	55
29.0	1.949258	55	55
30.0	1.949258	35	35
31.0	1.949258	33	33
32.0	1.949258	36	36
33.0	1.949258	33	33
34.0	1.949258	23	23
35.0	1.949258	25	25
36.0	1.949258	23	23
37.0	1.949258	21	21
38.0	1.949258	17	17
39.0	1.949258	18	18
40.0	1.949258	12	12
41.0	1.949258	20	20
42.0	1.949258	11	11
43.0	1.949258	17	17
44.0	1.949258	15	15
45.0	1.949258	13	13
46.0	1.949258	15	15
47.0	1.949258	16	16
48.0	1.949258	7	7
49.0	1.949258	12	12
50.0	1.949258	11	11
51.0	1.949258	22	22
52.0	1.949258	6	6
53.0	1.949258	12	12
54.0	1.949258	6	6
55.0	1.949258	11	11
56.0	1.949258	7	7
57.0	1.949258	9	9
58.0	1.949258	7	7
59.0	1.949258	5	5
60.0	1.949258	9	9
61.0	1.949258	9	9
62.0	1.949258	6	6
63.0	1.949258	6	6
64.0	1.949258	5	5
65.0	1.949258	6	6
66.0	1.949258	4	4
67.0	1.949258	3	3
68.0	1.949258	7	7
69.0	1.949258	4	4
70.0	1.949258	3	3
71.0	1.949258	6	6
72.0	1.949258	5	5
73.0	1.949258	4	4
74.0	1.949258	0	0
75.0	1.949258	2	2
76.0	1.949258	2	2
77.0	1.949258	3	3
78.0	1.949258	2	2
79.0	1.949258	0	0
80.0	1.949258	1	1
81.0	1.949258	6	6
82.0	1.949258	1	1
83.0	1.949258	4	4
84.0	1.949258	2	2
85.0	1.949258	1	1
86.0	1.949258	4	4
87.0	1.949258	1	1
88.0	1.949258	1	1
89.0	1.949258	1	1
90.0	1.949258	5	5
91.0	1.949258	2	2
92.0	1.949258	2	2
93.0	1.949258	4	4
94.0	1.949258	2	2
95.0	1.949258	3	3
96.0	1.949258	1	1
97.0	1.949258	3	3
98.0	1.949258	1	1
99.0	1.949258	3	3
100.0	1.949258	2	2
102.0	0	4	4
105.0	0	1	1
106.0	0	1	1
107.0	0	2	2
108.0	0	2	2
109.0	0	1	1
110.0	0	3	3
112.0	0	1	1
113.0	0	1	1
115.0	0	1	1
118.0	0	3	3
120.0	0	1	1
123.0	0	1	1
124.0	0	2	2
125.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
133.0	0	2	2
134.0	0	2	2
135.0	0	1	1
136.0	0	1	1
138.0	0	2	2
139.0	0	1	1
140.0	0	1	1
141.0	0	1	1
142.0	0	2	2
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
151.0	0	1	1
154.0	0	1	1
157.0	0	1	1
158.0	0	2	2
161.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	2	2
169.0	0	1	1
171.0	0	1	1
177.0	0	1	1
180.0	0	1	1
181.0	0	1	1
183.0	0	1	1
184.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
197.0	0	2	2
198.0	0	2	2
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
206.0	0	2	2
207.0	0	1	1
210.0	0	1	1
211.0	0	1	1
214.0	0	2	2
219.0	0	2	2
222.0	0	1	1
233.0	0	1	1
236.0	0	1	1
240.0	0	1	1
246.0	0	1	1
248.0	0	1	1
255.0	0	1	1
257.0	0	1	1
260.0	0	1	1
262.0	0	1	1
263.0	0	1	1
282.0	0	1	1
283.0	0	1	1
286.0	0	1	1
300.0	0	1	1