## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Pri_1_2016-09-03/UA_Kie_Pri_1_2016-09-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Pri_1_2016-09-03/UA_Kie_Pri_1_2016-09-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Pri_1_2016-09-03/UA_Kie_Pri_1_2016-09-03.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 16:48:28 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	34906255	4736662	0	0	8901111	238550	0	0.211318	45433202

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	4185553	4185553
2.0	1.900995	183635	183635
3.0	2.712787	11702	11702
4.0	3.444208	1414	1414
5.0	4.103214	512	512
6.0	4.696976	292	292
7.0	5.231952	227	227
8.0	5.713963	138	138
9.0	6.148252	137	137
10.0	6.539545	79	79
11.0	6.892097	88	88
12.0	7.209746	62	62
13.0	7.495945	37	37
14.0	7.753809	50	50
15.0	7.986144	39	39
16.0	8.195476	34	34
17.0	8.384083	37	37
18.0	8.554018	26	26
19.0	8.707127	23	23
20.0	8.845079	26	26
21.0	8.969372	22	22
22.0	9.08136	15	15
23.0	9.18226	10	10
24.0	9.273171	15	15
25.0	9.355081	9	9
26.0	9.428882	16	16
27.0	9.495376	10	10
28.0	9.555287	9	9
29.0	9.609266	18	18
30.0	9.657901	8	8
31.0	9.701721	13	13
32.0	9.741203	7	7
33.0	9.776775	13	13
34.0	9.808826	6	6
35.0	9.837704	5	5
36.0	9.863722	5	5
37.0	9.887165	7	7
38.0	9.908287	9	9
39.0	9.927317	6	6
40.0	9.944464	3	3
41.0	9.959912	4	4
42.0	9.973832	2	2
43.0	9.986373	7	7
44.0	9.997673	5	5
45.0	10.007854	0	0
46.0	10.017027	4	4
47.0	10.025291	1	1
48.0	10.032738	3	3
49.0	10.039447	3	3
50.0	10.045492	4	4
51.0	10.050939	2	2
52.0	10.055846	3	3
53.0	10.060267	2	2
54.0	10.064251	2	2
55.0	10.06784	2	2
56.0	10.071074	3	3
57.0	10.073988	3	3
58.0	10.076613	5	5
59.0	10.078979	5	5
60.0	10.08111	3	3
61.0	10.08303	5	5
62.0	10.08476	1	1
63.0	10.086319	5	5
64.0	10.087723	2	2
65.0	10.088989	0	0
66.0	10.090129	3	3
67.0	10.091156	2	2
68.0	10.092082	5	5
69.0	10.092916	1	1
70.0	10.093667	1	1
71.0	10.094344	0	0
72.0	10.094954	2	2
73.0	10.095504	2	2
74.0	10.095999	2	2
75.0	10.096445	2	2
76.0	10.096847	1	1
77.0	10.097209	0	0
78.0	10.097535	1	1
79.0	10.097829	0	0
80.0	10.098094	3	3
81.0	10.098333	1	1
82.0	10.098548	0	0
83.0	10.098742	1	1
84.0	10.098916	0	0
85.0	10.099073	1	1
86.0	10.099215	3	3
87.0	10.099343	1	1
88.0	10.099458	1	1
89.0	10.099562	0	0
90.0	10.099655	1	1
91.0	10.099739	0	0
92.0	10.099815	1	1
93.0	10.099883	1	1
94.0	10.099945	1	1
95.0	10.1	0	0
96.0	10.10005	0	0
97.0	10.100095	0	0
98.0	10.100136	1	1
99.0	10.100172	0	0
100.0	10.100205	1	1
103.0	0	1	1
108.0	0	1	1
113.0	0	1	1
123.0	0	1	1
127.0	0	2	2
148.0	0	1	1
168.0	0	1	1
379.0	0	1	1