## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-24/SE_Ska_Lun_1_2015-08-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-24/SE_Ska_Lun_1_2015-08-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/SE_Ska_Lun_1_2015-08-24/SE_Ska_Lun_1_2015-08-24.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 09:01:33 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	12517294	34278244	0	0	5401385	9183165	0	0.293162	51950223

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17926327	17926327
2.0	1.51694	5132520	5132520
3.0	1.784167	1329511	1329511
4.0	1.922307	319234	319234
5.0	1.993717	71190	71190
6.0	2.030632	15644	15644
7.0	2.049715	3394	3394
8.0	2.059579	851	851
9.0	2.064679	333	333
10.0	2.067315	202	202
11.0	2.068678	177	177
12.0	2.069382	129	129
13.0	2.069746	130	130
14.0	2.069934	113	113
15.0	2.070032	78	78
16.0	2.070082	82	82
17.0	2.070108	64	64
18.0	2.070121	90	90
19.0	2.070128	60	60
20.0	2.070132	48	48
21.0	2.070134	59	59
22.0	2.070135	49	49
23.0	2.070135	55	55
24.0	2.070136	39	39
25.0	2.070136	41	41
26.0	2.070136	26	26
27.0	2.070136	39	39
28.0	2.070136	32	32
29.0	2.070136	33	33
30.0	2.070136	19	19
31.0	2.070136	22	22
32.0	2.070136	20	20
33.0	2.070136	18	18
34.0	2.070136	13	13
35.0	2.070136	16	16
36.0	2.070136	18	18
37.0	2.070136	17	17
38.0	2.070136	14	14
39.0	2.070136	8	8
40.0	2.070136	10	10
41.0	2.070136	12	12
42.0	2.070136	10	10
43.0	2.070136	7	7
44.0	2.070136	13	13
45.0	2.070136	7	7
46.0	2.070136	3	3
47.0	2.070136	9	9
48.0	2.070136	3	3
49.0	2.070136	7	7
50.0	2.070136	6	6
51.0	2.070136	3	3
52.0	2.070136	3	3
53.0	2.070136	7	7
54.0	2.070136	9	9
55.0	2.070136	2	2
56.0	2.070136	3	3
57.0	2.070136	4	4
58.0	2.070136	6	6
59.0	2.070136	5	5
60.0	2.070136	4	4
61.0	2.070136	3	3
62.0	2.070136	4	4
63.0	2.070136	2	2
64.0	2.070136	4	4
65.0	2.070136	2	2
66.0	2.070136	1	1
67.0	2.070136	2	2
68.0	2.070136	3	3
69.0	2.070136	3	3
70.0	2.070136	1	1
71.0	2.070136	4	4
72.0	2.070136	1	1
73.0	2.070136	3	3
74.0	2.070136	4	4
75.0	2.070136	0	0
76.0	2.070136	3	3
77.0	2.070136	0	0
78.0	2.070136	2	2
79.0	2.070136	1	1
80.0	2.070136	2	2
81.0	2.070136	4	4
82.0	2.070136	0	0
83.0	2.070136	1	1
84.0	2.070136	4	4
85.0	2.070136	0	0
86.0	2.070136	2	2
87.0	2.070136	0	0
88.0	2.070136	1	1
89.0	2.070136	0	0
90.0	2.070136	1	1
91.0	2.070136	3	3
92.0	2.070136	2	2
93.0	2.070136	0	0
94.0	2.070136	1	1
95.0	2.070136	0	0
96.0	2.070136	1	1
97.0	2.070136	0	0
98.0	2.070136	1	1
99.0	2.070136	1	1
100.0	2.070136	0	0
102.0	0	1	1
103.0	0	2	2
105.0	0	1	1
108.0	0	1	1
109.0	0	2	2
113.0	0	1	1
116.0	0	2	2
117.0	0	1	1
123.0	0	1	1
140.0	0	1	1
148.0	0	1	1