## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/BY_Bre_Bre_1_2015-09-11/BY_Bre_Bre_1_2015-09-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/BY_Bre_Bre_1_2015-09-11/BY_Bre_Bre_1_2015-09-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/BY_Bre_Bre_1_2015-09-11/BY_Bre_Bre_1_2015-09-11.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 08:39:09 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	8623603	30467987	0	0	3365901	2995250	0	0.134509	144629988

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	24489377	24489377
2.0	1.810048	2381888	2381888
3.0	2.466226	226441	226441
4.0	2.997762	24129	24129
5.0	3.428331	3338	3338
6.0	3.777113	816	816
7.0	4.059644	388	388
8.0	4.288507	290	290
9.0	4.473897	235	235
10.0	4.624072	182	182
11.0	4.745721	166	166
12.0	4.844262	154	154
13.0	4.924085	132	132
14.0	4.988746	111	111
15.0	5.041125	104	104
16.0	5.083553	96	96
17.0	5.117923	86	86
18.0	5.145764	76	76
19.0	5.168316	70	70
20.0	5.186585	74	74
21.0	5.201384	78	78
22.0	5.213371	54	54
23.0	5.223081	45	45
24.0	5.230947	39	39
25.0	5.237319	44	44
26.0	5.242481	48	48
27.0	5.246662	31	31
28.0	5.250048	48	48
29.0	5.252792	36	36
30.0	5.255014	32	32
31.0	5.256814	25	25
32.0	5.258273	25	25
33.0	5.259454	39	39
34.0	5.260411	23	23
35.0	5.261186	19	19
36.0	5.261814	31	31
37.0	5.262322	37	37
38.0	5.262734	22	22
39.0	5.263068	13	13
40.0	5.263339	18	18
41.0	5.263558	21	21
42.0	5.263735	16	16
43.0	5.263879	16	16
44.0	5.263995	13	13
45.0	5.264089	16	16
46.0	5.264166	13	13
47.0	5.264228	12	12
48.0	5.264278	11	11
49.0	5.264318	13	13
50.0	5.264351	9	9
51.0	5.264378	11	11
52.0	5.264399	6	6
53.0	5.264417	6	6
54.0	5.264431	9	9
55.0	5.264442	9	9
56.0	5.264452	10	10
57.0	5.264459	6	6
58.0	5.264465	10	10
59.0	5.26447	9	9
60.0	5.264474	5	5
61.0	5.264478	6	6
62.0	5.26448	5	5
63.0	5.264482	6	6
64.0	5.264484	5	5
65.0	5.264485	5	5
66.0	5.264487	3	3
67.0	5.264488	7	7
68.0	5.264488	3	3
69.0	5.264489	4	4
70.0	5.264489	4	4
71.0	5.26449	5	5
72.0	5.26449	4	4
73.0	5.26449	6	6
74.0	5.264491	2	2
75.0	5.264491	2	2
76.0	5.264491	3	3
77.0	5.264491	6	6
78.0	5.264491	7	7
79.0	5.264491	4	4
80.0	5.264491	6	6
81.0	5.264491	5	5
82.0	5.264491	2	2
83.0	5.264491	4	4
84.0	5.264491	6	6
85.0	5.264491	0	0
86.0	5.264491	2	2
87.0	5.264491	0	0
88.0	5.264491	2	2
89.0	5.264491	3	3
90.0	5.264491	2	2
91.0	5.264491	2	2
92.0	5.264491	2	2
93.0	5.264491	2	2
94.0	5.264491	0	0
95.0	5.264491	3	3
96.0	5.264491	3	3
97.0	5.264491	3	3
98.0	5.264491	3	3
99.0	5.264491	4	4
100.0	5.264491	1	1
101.0	0	2	2
102.0	0	1	1
103.0	0	2	2
104.0	0	5	5
106.0	0	1	1
107.0	0	2	2
109.0	0	1	1
110.0	0	1	1
113.0	0	2	2
114.0	0	1	1
115.0	0	1	1
116.0	0	1	1
119.0	0	3	3
120.0	0	1	1
121.0	0	1	1
122.0	0	1	1
126.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
133.0	0	1	1
134.0	0	1	1
136.0	0	1	1
139.0	0	1	1
140.0	0	2	2
141.0	0	1	1
142.0	0	1	1
145.0	0	1	1
148.0	0	1	1
149.0	0	1	1
153.0	0	1	1
154.0	0	1	1
167.0	0	1	1
184.0	0	1	1
187.0	0	1	1
191.0	0	1	1
196.0	0	1	1
222.0	0	1	1
278.0	0	1	1
294.0	0	1	1
315.0	0	1	1