## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-07-15/US_Pen_Lin_1_2011-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-07-15/US_Pen_Lin_1_2011-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-07-15/US_Pen_Lin_1_2011-07-15.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 17:39:05 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	103760	39466247	0	0	38664	223746	0	0.006151	3467530435

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	38773089	38773089
2.0	1.988683	178515	178515
3.0	2.966177	15789	15789
4.0	3.932608	1509	1509
5.0	4.888102	245	245
6.0	5.832783	77	77
7.0	6.766773	40	40
8.0	7.690192	20	20
9.0	8.603161	24	24
10.0	9.505798	6	6
11.0	10.39822	13	13
12.0	11.280542	7	7
13.0	12.152878	3	3
14.0	13.015343	6	6
15.0	13.868046	5	5
16.0	14.7111	6	6
17.0	15.544612	4	4
18.0	16.368692	5	5
19.0	17.183445	4	4
20.0	17.988978	2	2
21.0	18.785394	3	3
22.0	19.572797	5	5
23.0	20.351289	3	3
24.0	21.120971	3	3
25.0	21.881942	2	2
26.0	22.634302	1	1
27.0	23.378146	0	0
28.0	24.113573	2	2
29.0	24.840676	1	1
30.0	25.559551	1	1
31.0	26.27029	2	2
32.0	26.972986	3	3
33.0	27.667729	1	1
34.0	28.354609	1	1
35.0	29.033717	1	1
36.0	29.705138	0	0
37.0	30.368961	0	0
38.0	31.025272	0	0
39.0	31.674155	2	2
40.0	32.315694	2	2
41.0	32.949973	0	0
42.0	33.577074	1	1
43.0	34.197078	0	0
44.0	34.810065	1	1
45.0	35.416115	3	3
46.0	36.015306	1	1
47.0	36.607716	0	0
48.0	37.193421	0	0
49.0	37.772499	0	0
50.0	38.345022	1	1
51.0	38.911066	0	0
52.0	39.470705	0	0
53.0	40.02401	0	0
54.0	40.571053	0	0
55.0	41.111905	0	0
56.0	41.646636	1	1
57.0	42.175315	0	0
58.0	42.698012	0	0
59.0	43.214793	0	0
60.0	43.725725	0	0
61.0	44.230875	0	0
62.0	44.730309	0	0
63.0	45.22409	1	1
64.0	45.712283	0	0
65.0	46.194951	1	1
66.0	46.672156	0	0
67.0	47.143961	0	0
68.0	47.610427	0	0
69.0	48.071613	0	0
70.0	48.527581	1	1
71.0	48.978388	3	3
72.0	49.424093	0	0
73.0	49.864754	0	0
74.0	50.300428	0	0
75.0	50.731171	0	0
76.0	51.15704	0	0
77.0	51.578089	0	0
78.0	51.994373	0	0
79.0	52.405945	0	0
80.0	52.81286	2	2
81.0	53.21517	0	0
82.0	53.612927	0	0
83.0	54.006183	0	0
84.0	54.394987	0	0
85.0	54.779392	0	0
86.0	55.159447	0	0
87.0	55.5352	0	0
88.0	55.906701	0	0
89.0	56.273997	0	0
90.0	56.637137	0	0
91.0	56.996167	1	1
92.0	57.351134	0	0
93.0	57.702083	0	0
94.0	58.049061	0	0
95.0	58.392112	0	0
96.0	58.731281	1	1
97.0	59.066611	0	0
98.0	59.398147	0	0
99.0	59.72593	0	0
100.0	60.050004	0	0
101.0	0	1	1
103.0	0	1	1
113.0	0	1	1
117.0	0	1	1
127.0	0	1	1
129.0	0	1	1
130.0	0	2	2
134.0	0	1	1
138.0	0	1	1
146.0	0	1	1
155.0	0	1	1
187.0	0	1	1
197.0	0	1	1
228.0	0	1	1
2273.0	0	1	1