## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-05-07/US_Cal_Esp_1_2013-05-07.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-05-07/US_Cal_Esp_1_2013-05-07.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-05-07/US_Cal_Esp_1_2013-05-07.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 17:46:38 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	2693908	41221392	0	0	1120026	1501380	0	0.048425	552054908

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	37583326	37583326
2.0	1.928051	1307211	1307211
3.0	2.789329	47378	47378
4.0	3.588638	4175	4175
5.0	4.330438	1360	1360
6.0	5.018865	741	741
7.0	5.657761	437	437
8.0	6.250689	329	329
9.0	6.800955	215	215
10.0	7.311631	164	164
11.0	7.785564	121	121
12.0	8.225397	123	123
13.0	8.633585	99	99
14.0	9.012404	85	85
15.0	9.363967	80	80
16.0	9.690235	67	67
17.0	9.993029	60	60
18.0	10.274036	61	61
19.0	10.534826	43	43
20.0	10.776851	46	46
21.0	11.001464	31	31
22.0	11.209915	29	29
23.0	11.403369	23	23
24.0	11.582903	34	34
25.0	11.74952	20	20
26.0	11.90415	24	24
27.0	12.047653	32	32
28.0	12.180832	17	17
29.0	12.304429	20	20
30.0	12.419133	19	19
31.0	12.525584	20	20
32.0	12.624376	13	13
33.0	12.716059	17	17
34.0	12.801147	16	16
35.0	12.880112	16	16
36.0	12.953396	10	10
37.0	13.021407	14	14
38.0	13.084525	4	4
39.0	13.143101	5	5
40.0	13.197463	8	8
41.0	13.247914	9	9
42.0	13.294735	9	9
43.0	13.338187	3	3
44.0	13.378512	6	6
45.0	13.415936	5	5
46.0	13.450668	7	7
47.0	13.482901	10	10
48.0	13.512814	3	3
49.0	13.540576	5	5
50.0	13.56634	3	3
51.0	13.59025	8	8
52.0	13.61244	7	7
53.0	13.633033	2	2
54.0	13.652145	4	4
55.0	13.669881	3	3
56.0	13.686342	4	4
57.0	13.701618	4	4
58.0	13.715795	2	2
59.0	13.728952	5	5
60.0	13.741162	2	2
61.0	13.752494	4	4
62.0	13.76301	1	1
63.0	13.77277	3	3
64.0	13.781828	1	1
65.0	13.790234	5	5
66.0	13.798035	3	3
67.0	13.805275	4	4
68.0	13.811994	1	1
69.0	13.818229	0	0
70.0	13.824016	2	2
71.0	13.829387	2	2
72.0	13.834371	2	2
73.0	13.838996	2	2
74.0	13.843289	2	2
75.0	13.847273	0	0
76.0	13.85097	2	2
77.0	13.854401	2	2
78.0	13.857586	0	0
79.0	13.860541	0	0
80.0	13.863283	1	1
81.0	13.865829	1	1
82.0	13.868191	2	2
83.0	13.870383	3	3
84.0	13.872417	1	1
85.0	13.874305	0	0
86.0	13.876058	1	1
87.0	13.877684	1	1
88.0	13.879193	2	2
89.0	13.880594	1	1
90.0	13.881893	1	1
91.0	13.8831	0	0
92.0	13.884219	1	1
93.0	13.885258	0	0
94.0	13.886222	1	1
95.0	13.887117	2	2
96.0	13.887948	0	0
97.0	13.888718	1	1
98.0	13.889434	0	0
99.0	13.890097	1	1
100.0	13.890713	0	0
102.0	0	1	1
103.0	0	1	1
104.0	0	4	4
107.0	0	1	1
108.0	0	1	1
110.0	0	1	1
112.0	0	1	1
113.0	0	2	2
116.0	0	2	2
117.0	0	2	2
118.0	0	1	1
119.0	0	1	1
121.0	0	1	1
127.0	0	1	1
129.0	0	2	2
130.0	0	1	1
132.0	0	1	1
135.0	0	1	1
136.0	0	1	1
146.0	0	1	1
147.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	1	1
157.0	0	1	1
159.0	0	2	2
172.0	0	1	1
176.0	0	2	2
181.0	0	1	1
188.0	0	1	1
201.0	0	1	1
205.0	0	1	1
213.0	0	1	1
222.0	0	1	1
229.0	0	1	1
239.0	0	2	2
242.0	0	1	1
248.0	0	1	1
250.0	0	2	2
254.0	0	1	1
257.0	0	1	1
260.0	0	1	1
264.0	0	1	1
270.0	0	1	1
271.0	0	1	1
275.0	0	1	1
278.0	0	1	1
282.0	0	1	1
283.0	0	1	1
318.0	0	1	1
331.0	0	1	1
355.0	0	1	1
367.0	0	1	1
370.0	0	1	1
372.0	0	1	1
373.0	0	1	1
404.0	0	1	1
409.0	0	1	1
425.0	0	1	1
444.0	0	1	1
462.0	0	1	1
508.0	0	1	1
523.0	0	1	1
549.0	0	1	1
559.0	0	1	1
594.0	0	1	1
607.0	0	1	1
611.0	0	1	1
643.0	0	1	1
784.0	0	1	1
807.0	0	1	1
836.0	0	1	1
864.0	0	1	1
942.0	0	1	1
958.0	0	1	1
979.0	0	1	1
1022.0	0	1	1
1041.0	0	1	1
1561.0	0	1	1
1734.0	0	1	1
1778.0	0	1	1
1851.0	0	1	1
1916.0	0	1	1
3313.0	0	1	1