## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-07-28/TR_Ank_Yes_1_2015-07-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-07-28/TR_Ank_Yes_1_2015-07-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-07-28/TR_Ank_Yes_1_2015-07-28.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 09:05:51 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	12563356	37534539	0	0	5781572	6613577	0	0.216914	93593189

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25083367	25083367
2.0	1.669624	4580525	4580525
3.0	2.11802	768726	768726
4.0	2.418276	122859	122859
5.0	2.619335	19346	19346
6.0	2.753969	3286	3286
7.0	2.844123	771	771
8.0	2.904493	267	267
9.0	2.944917	194	194
10.0	2.971987	135	135
11.0	2.990113	102	102
12.0	3.002251	104	104
13.0	3.010379	86	86
14.0	3.015821	71	71
15.0	3.019466	65	65
16.0	3.021906	49	49
17.0	3.02354	54	54
18.0	3.024635	30	30
19.0	3.025367	36	36
20.0	3.025858	27	27
21.0	3.026186	23	23
22.0	3.026406	20	20
23.0	3.026554	34	34
24.0	3.026652	28	28
25.0	3.026719	25	25
26.0	3.026763	15	15
27.0	3.026792	10	10
28.0	3.026812	15	15
29.0	3.026826	14	14
30.0	3.026834	16	16
31.0	3.02684	14	14
32.0	3.026844	10	10
33.0	3.026847	9	9
34.0	3.026849	13	13
35.0	3.02685	4	4
36.0	3.026851	10	10
37.0	3.026851	9	9
38.0	3.026852	4	4
39.0	3.026852	2	2
40.0	3.026852	9	9
41.0	3.026852	6	6
42.0	3.026852	3	3
43.0	3.026852	6	6
44.0	3.026852	4	4
45.0	3.026852	1	1
46.0	3.026852	2	2
47.0	3.026852	5	5
48.0	3.026852	4	4
49.0	3.026852	5	5
50.0	3.026852	3	3
51.0	3.026852	4	4
52.0	3.026852	6	6
53.0	3.026852	3	3
54.0	3.026852	1	1
55.0	3.026852	0	0
56.0	3.026852	2	2
57.0	3.026852	2	2
58.0	3.026852	1	1
59.0	3.026852	4	4
60.0	3.026852	0	0
61.0	3.026852	2	2
62.0	3.026852	1	1
63.0	3.026852	2	2
64.0	3.026852	2	2
65.0	3.026852	0	0
66.0	3.026852	2	2
67.0	3.026852	0	0
68.0	3.026852	0	0
69.0	3.026852	1	1
70.0	3.026852	2	2
71.0	3.026852	2	2
72.0	3.026852	2	2
73.0	3.026852	0	0
74.0	3.026852	5	5
75.0	3.026852	1	1
76.0	3.026852	2	2
77.0	3.026852	0	0
78.0	3.026852	2	2
79.0	3.026852	0	0
80.0	3.026852	1	1
81.0	3.026852	0	0
82.0	3.026852	1	1
83.0	3.026852	1	1
84.0	3.026852	0	0
85.0	3.026852	3	3
86.0	3.026852	0	0
87.0	3.026852	0	0
88.0	3.026852	1	1
89.0	3.026852	2	2
90.0	3.026852	0	0
91.0	3.026852	1	1
92.0	3.026852	0	0
93.0	3.026852	1	1
94.0	3.026852	0	0
95.0	3.026852	1	1
96.0	3.026852	1	1
97.0	3.026852	0	0
98.0	3.026852	3	3
99.0	3.026852	0	0
100.0	3.026852	0	0
106.0	0	1	1
107.0	0	1	1
110.0	0	1	1
115.0	0	1	1
119.0	0	1	1
153.0	0	1	1
154.0	0	1	1
164.0	0	1	1
175.0	0	1	1
323.0	0	1	1
370.0	0	1	1