## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-05-01/TR_Ank_Yes_1_2015-05-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-05-01/TR_Ank_Yes_1_2015-05-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-05-01/TR_Ank_Yes_1_2015-05-01.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 08:55:43 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	9333689	34066393	0	0	3886901	8801064	0	0.277398	54004451

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18295190	18295190
2.0	1.532162	5045687	5045687
3.0	1.815359	1253439	1253439
4.0	1.966065	285338	285338
5.0	2.046265	60738	60738
6.0	2.088945	12706	12706
7.0	2.111657	2773	2773
8.0	2.123744	717	717
9.0	2.130176	294	294
10.0	2.133599	192	192
11.0	2.13542	181	181
12.0	2.13639	144	144
13.0	2.136906	124	124
14.0	2.13718	116	116
15.0	2.137326	125	125
16.0	2.137404	122	122
17.0	2.137445	91	91
18.0	2.137467	95	95
19.0	2.137479	71	71
20.0	2.137485	76	76
21.0	2.137489	52	52
22.0	2.13749	62	62
23.0	2.137491	50	50
24.0	2.137492	53	53
25.0	2.137492	47	47
26.0	2.137492	31	31
27.0	2.137492	52	52
28.0	2.137492	37	37
29.0	2.137492	30	30
30.0	2.137492	42	42
31.0	2.137492	26	26
32.0	2.137492	30	30
33.0	2.137492	26	26
34.0	2.137492	26	26
35.0	2.137492	25	25
36.0	2.137492	27	27
37.0	2.137492	22	22
38.0	2.137492	17	17
39.0	2.137492	21	21
40.0	2.137492	19	19
41.0	2.137492	16	16
42.0	2.137492	15	15
43.0	2.137492	16	16
44.0	2.137492	13	13
45.0	2.137492	15	15
46.0	2.137492	13	13
47.0	2.137492	10	10
48.0	2.137492	9	9
49.0	2.137492	16	16
50.0	2.137492	11	11
51.0	2.137492	18	18
52.0	2.137492	9	9
53.0	2.137492	9	9
54.0	2.137492	11	11
55.0	2.137492	7	7
56.0	2.137492	9	9
57.0	2.137492	6	6
58.0	2.137492	7	7
59.0	2.137492	3	3
60.0	2.137492	6	6
61.0	2.137492	5	5
62.0	2.137492	5	5
63.0	2.137492	2	2
64.0	2.137492	6	6
65.0	2.137492	3	3
66.0	2.137492	1	1
67.0	2.137492	7	7
68.0	2.137492	4	4
69.0	2.137492	3	3
70.0	2.137492	3	3
71.0	2.137492	5	5
72.0	2.137492	6	6
73.0	2.137492	1	1
74.0	2.137492	5	5
75.0	2.137492	2	2
76.0	2.137492	1	1
77.0	2.137492	3	3
78.0	2.137492	2	2
79.0	2.137492	2	2
80.0	2.137492	3	3
81.0	2.137492	2	2
82.0	2.137492	1	1
83.0	2.137492	5	5
84.0	2.137492	5	5
85.0	2.137492	8	8
86.0	2.137492	1	1
87.0	2.137492	3	3
88.0	2.137492	2	2
89.0	2.137492	2	2
90.0	2.137492	1	1
91.0	2.137492	3	3
92.0	2.137492	3	3
93.0	2.137492	0	0
94.0	2.137492	3	3
95.0	2.137492	4	4
96.0	2.137492	1	1
97.0	2.137492	3	3
98.0	2.137492	1	1
99.0	2.137492	1	1
100.0	2.137492	1	1
102.0	0	4	4
103.0	0	2	2
104.0	0	2	2
106.0	0	2	2
108.0	0	2	2
109.0	0	1	1
111.0	0	2	2
112.0	0	1	1
113.0	0	2	2
114.0	0	1	1
116.0	0	1	1
117.0	0	1	1
119.0	0	2	2
120.0	0	1	1
122.0	0	1	1
124.0	0	1	1
126.0	0	1	1
129.0	0	2	2
133.0	0	1	1
136.0	0	1	1
138.0	0	1	1
139.0	0	1	1
143.0	0	2	2
146.0	0	1	1
149.0	0	1	1
153.0	0	1	1
154.0	0	1	1
169.0	0	1	1
197.0	0	1	1
206.0	0	1	1
580.0	0	1	1