## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Cor_1_2015-08-08/ES_Gra_Cor_1_2015-08-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Cor_1_2015-08-08/ES_Gra_Cor_1_2015-08-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Cor_1_2015-08-08/ES_Gra_Cor_1_2015-08-08.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 09:08:11 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	7556486	31074550	0	0	3359419	4585257	0	0.179755	94661823

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22173074	22173074
2.0	1.720169	3321836	3321836
3.0	2.238813	463893	463893
4.0	2.612324	64545	64545
5.0	2.881315	9723	9723
6.0	3.075035	1857	1857
7.0	3.214545	624	624
8.0	3.315016	382	382
9.0	3.387373	285	285
10.0	3.439482	217	217
11.0	3.477009	183	183
12.0	3.504035	155	155
13.0	3.523498	137	137
14.0	3.537515	143	143
15.0	3.547609	123	123
16.0	3.554879	93	93
17.0	3.560114	100	100
18.0	3.563885	96	96
19.0	3.5666	67	67
20.0	3.568555	69	69
21.0	3.569964	89	89
22.0	3.570978	63	63
23.0	3.571708	49	49
24.0	3.572234	60	60
25.0	3.572613	62	62
26.0	3.572886	58	58
27.0	3.573082	47	47
28.0	3.573224	46	46
29.0	3.573326	38	38
30.0	3.573399	38	38
31.0	3.573452	45	45
32.0	3.57349	34	34
33.0	3.573518	30	30
34.0	3.573537	32	32
35.0	3.573552	31	31
36.0	3.573562	26	26
37.0	3.573569	23	23
38.0	3.573574	28	28
39.0	3.573578	21	21
40.0	3.573581	27	27
41.0	3.573583	17	17
42.0	3.573584	18	18
43.0	3.573585	16	16
44.0	3.573586	20	20
45.0	3.573587	20	20
46.0	3.573587	16	16
47.0	3.573587	16	16
48.0	3.573588	18	18
49.0	3.573588	13	13
50.0	3.573588	12	12
51.0	3.573588	11	11
52.0	3.573588	20	20
53.0	3.573588	7	7
54.0	3.573588	8	8
55.0	3.573588	8	8
56.0	3.573588	6	6
57.0	3.573588	10	10
58.0	3.573588	10	10
59.0	3.573588	15	15
60.0	3.573588	10	10
61.0	3.573588	10	10
62.0	3.573588	12	12
63.0	3.573588	9	9
64.0	3.573588	8	8
65.0	3.573588	4	4
66.0	3.573588	6	6
67.0	3.573588	9	9
68.0	3.573588	8	8
69.0	3.573588	7	7
70.0	3.573588	8	8
71.0	3.573588	11	11
72.0	3.573588	8	8
73.0	3.573588	5	5
74.0	3.573588	6	6
75.0	3.573588	6	6
76.0	3.573588	4	4
77.0	3.573588	7	7
78.0	3.573588	6	6
79.0	3.573588	3	3
80.0	3.573588	2	2
81.0	3.573588	4	4
82.0	3.573588	5	5
83.0	3.573588	5	5
84.0	3.573588	5	5
85.0	3.573588	0	0
86.0	3.573588	2	2
87.0	3.573588	3	3
88.0	3.573588	1	1
89.0	3.573588	7	7
90.0	3.573588	6	6
91.0	3.573588	3	3
92.0	3.573588	0	0
93.0	3.573588	1	1
94.0	3.573588	3	3
95.0	3.573588	3	3
96.0	3.573588	4	4
97.0	3.573588	0	0
98.0	3.573588	3	3
99.0	3.573588	1	1
100.0	3.573588	1	1
101.0	0	3	3
102.0	0	2	2
103.0	0	3	3
104.0	0	1	1
105.0	0	2	2
106.0	0	2	2
108.0	0	1	1
109.0	0	2	2
110.0	0	1	1
111.0	0	2	2
112.0	0	2	2
113.0	0	3	3
115.0	0	2	2
116.0	0	4	4
117.0	0	3	3
119.0	0	1	1
120.0	0	5	5
121.0	0	1	1
123.0	0	2	2
124.0	0	1	1
125.0	0	3	3
129.0	0	4	4
130.0	0	1	1
131.0	0	1	1
132.0	0	2	2
133.0	0	1	1
136.0	0	1	1
139.0	0	1	1
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
145.0	0	1	1
148.0	0	2	2
150.0	0	1	1
151.0	0	2	2
153.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	1	1
157.0	0	5	5
159.0	0	1	1
161.0	0	2	2
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
172.0	0	1	1
173.0	0	2	2
175.0	0	2	2
176.0	0	1	1
177.0	0	1	1
185.0	0	1	1
190.0	0	1	1
194.0	0	1	1
196.0	0	1	1
200.0	0	1	1
204.0	0	1	1
205.0	0	1	1
210.0	0	1	1
211.0	0	2	2
220.0	0	1	1
228.0	0	1	1
253.0	0	1	1
259.0	0	1	1
265.0	0	1	1
278.0	0	1	1
375.0	0	1	1
396.0	0	1	1