## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2015-09-28/PL_War_Brz_1_2015-09-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2015-09-28/PL_War_Brz_1_2015-09-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2015-09-28/PL_War_Brz_1_2015-09-28.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 08:55:16 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	12392277	28914001	0	0	4437887	2478223	0	0.133784	158890812

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23826188	23826188
2.0	1.833623	2049409	2049409
3.0	2.52855	156324	156324
4.0	3.107858	12949	12949
5.0	3.590782	1970	1970
6.0	3.993358	814	814
7.0	4.328955	495	495
8.0	4.608717	393	393
9.0	4.841932	310	310
10.0	5.036346	228	228
11.0	5.198414	190	190
12.0	5.333517	150	150
13.0	5.446143	132	132
14.0	5.54003	121	121
15.0	5.618296	113	113
16.0	5.683541	96	96
17.0	5.73793	86	86
18.0	5.783271	72	72
19.0	5.821067	75	75
20.0	5.852576	59	59
21.0	5.878842	53	53
22.0	5.900737	33	33
23.0	5.91899	47	47
24.0	5.934207	37	37
25.0	5.946891	25	25
26.0	5.957465	32	32
27.0	5.96628	24	24
28.0	5.973628	23	23
29.0	5.979754	24	24
30.0	5.98486	30	30
31.0	5.989117	13	13
32.0	5.992666	19	19
33.0	5.995624	18	18
34.0	5.99809	20	20
35.0	6.000146	12	12
36.0	6.001859	19	19
37.0	6.003288	12	12
38.0	6.004479	14	14
39.0	6.005472	12	12
40.0	6.006299	15	15
41.0	6.006989	9	9
42.0	6.007564	11	11
43.0	6.008044	9	9
44.0	6.008443	15	15
45.0	6.008777	9	9
46.0	6.009054	5	5
47.0	6.009286	5	5
48.0	6.009479	10	10
49.0	6.00964	8	8
50.0	6.009774	8	8
51.0	6.009886	7	7
52.0	6.009979	11	11
53.0	6.010057	9	9
54.0	6.010121	5	5
55.0	6.010175	11	11
56.0	6.01022	9	9
57.0	6.010258	3	3
58.0	6.010289	3	3
59.0	6.010315	3	3
60.0	6.010337	3	3
61.0	6.010355	10	10
62.0	6.01037	6	6
63.0	6.010383	2	2
64.0	6.010393	3	3
65.0	6.010402	2	2
66.0	6.010409	2	2
67.0	6.010415	2	2
68.0	6.01042	4	4
69.0	6.010425	7	7
70.0	6.010428	6	6
71.0	6.010431	5	5
72.0	6.010434	3	3
73.0	6.010436	2	2
74.0	6.010437	2	2
75.0	6.010439	5	5
76.0	6.01044	5	5
77.0	6.010441	2	2
78.0	6.010442	2	2
79.0	6.010442	1	1
80.0	6.010443	6	6
81.0	6.010443	2	2
82.0	6.010444	0	0
83.0	6.010444	2	2
84.0	6.010444	5	5
85.0	6.010445	2	2
86.0	6.010445	0	0
87.0	6.010445	2	2
88.0	6.010445	3	3
89.0	6.010445	4	4
90.0	6.010445	0	0
91.0	6.010445	4	4
92.0	6.010446	5	5
93.0	6.010446	1	1
94.0	6.010446	6	6
95.0	6.010446	1	1
96.0	6.010446	0	0
97.0	6.010446	5	5
98.0	6.010446	0	0
99.0	6.010446	2	2
100.0	6.010446	1	1
103.0	0	1	1
104.0	0	2	2
105.0	0	2	2
106.0	0	2	2
109.0	0	2	2
112.0	0	3	3
113.0	0	1	1
114.0	0	1	1
116.0	0	2	2
119.0	0	1	1
120.0	0	1	1
121.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
136.0	0	2	2
138.0	0	2	2
140.0	0	1	1
141.0	0	1	1
142.0	0	1	1
146.0	0	1	1
149.0	0	1	1
161.0	0	1	1
166.0	0	1	1
175.0	0	1	1
178.0	0	1	1
185.0	0	2	2
191.0	0	1	1
194.0	0	1	1
196.0	0	1	1
197.0	0	1	1
211.0	0	1	1
217.0	0	1	1
218.0	0	1	1
225.0	0	1	1
228.0	0	1	1
230.0	0	1	1
233.0	0	1	1
234.0	0	1	1
266.0	0	1	1
298.0	0	1	1
304.0	0	1	1
320.0	0	1	1
341.0	0	1	1
493.0	0	1	1
530.0	0	1	1
674.0	0	1	1