## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2015-07-07/GB_Nor_Mar_1_2015-07-07.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2015-07-07/GB_Nor_Mar_1_2015-07-07.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Nor_Mar_1_2015-07-07/GB_Nor_Mar_1_2015-07-07.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 08:42:21 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	8050668	32307231	0	0	3444529	2824553	0	0.125144	173831249

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26601327	26601327
2.0	1.830395	2377678	2377678
3.0	2.51995	183190	183190
4.0	3.092554	14794	14794
5.0	3.568041	1827	1827
6.0	3.962883	572	572
7.0	4.290757	312	312
8.0	4.563023	235	235
9.0	4.78911	158	158
10.0	4.976853	124	124
11.0	5.132753	89	89
12.0	5.262211	82	82
13.0	5.369713	67	67
14.0	5.458982	55	55
15.0	5.53311	52	52
16.0	5.594666	38	38
17.0	5.645782	37	37
18.0	5.688228	40	40
19.0	5.723475	38	38
20.0	5.752744	16	16
21.0	5.777049	19	19
22.0	5.797232	18	18
23.0	5.813991	19	19
24.0	5.827908	16	16
25.0	5.839465	12	12
26.0	5.849062	19	19
27.0	5.85703	10	10
28.0	5.863648	9	9
29.0	5.869143	14	14
30.0	5.873706	8	8
31.0	5.877495	8	8
32.0	5.880642	6	6
33.0	5.883254	11	11
34.0	5.885424	6	6
35.0	5.887226	4	4
36.0	5.888722	5	5
37.0	5.889964	4	4
38.0	5.890996	5	5
39.0	5.891852	3	3
40.0	5.892564	2	2
41.0	5.893155	4	4
42.0	5.893645	3	3
43.0	5.894052	7	7
44.0	5.894391	1	1
45.0	5.894672	4	4
46.0	5.894905	4	4
47.0	5.895099	3	3
48.0	5.895259	3	3
49.0	5.895393	5	5
50.0	5.895504	5	5
51.0	5.895596	6	6
52.0	5.895672	2	2
53.0	5.895736	1	1
54.0	5.895789	4	4
55.0	5.895832	5	5
56.0	5.895869	2	2
57.0	5.895899	0	0
58.0	5.895924	2	2
59.0	5.895945	5	5
60.0	5.895962	0	0
61.0	5.895976	1	1
62.0	5.895988	0	0
63.0	5.895998	4	4
64.0	5.896007	2	2
65.0	5.896013	1	1
66.0	5.896019	1	1
67.0	5.896024	0	0
68.0	5.896028	0	0
69.0	5.896031	0	0
70.0	5.896034	1	1
71.0	5.896036	1	1
72.0	5.896038	0	0
73.0	5.896039	1	1
74.0	5.896041	1	1
75.0	5.896042	0	0
76.0	5.896042	1	1
77.0	5.896043	0	0
78.0	5.896044	1	1
79.0	5.896044	1	1
80.0	5.896045	0	0
81.0	5.896045	0	0
82.0	5.896045	0	0
83.0	5.896046	0	0
84.0	5.896046	2	2
85.0	5.896046	0	0
86.0	5.896046	1	1
87.0	5.896046	0	0
88.0	5.896046	1	1
89.0	5.896046	0	0
90.0	5.896046	2	2
91.0	5.896047	0	0
92.0	5.896047	0	0
93.0	5.896047	0	0
94.0	5.896047	0	0
95.0	5.896047	1	1
96.0	5.896047	0	0
97.0	5.896047	0	0
98.0	5.896047	0	0
99.0	5.896047	0	0
100.0	5.896047	0	0
105.0	0	1	1
106.0	0	1	1
107.0	0	3	3
108.0	0	1	1
109.0	0	1	1
120.0	0	1	1
124.0	0	1	1
129.0	0	2	2
135.0	0	1	1
137.0	0	1	1
143.0	0	1	1
187.0	0	1	1
332.0	0	1	1
389.0	0	1	1
504.0	0	1	1