## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2015-09-15/RU_Vla_Ale_1_2015-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2015-09-15/RU_Vla_Ale_1_2015-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Vla_Ale_1_2015-09-15/RU_Vla_Ale_1_2015-09-15.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 08:29:04 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	8049143	30254382	0	0	3308576	8312965	0	0.290769	44424312

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15556003	15556003
2.0	1.506094	4585703	4585703
3.0	1.762226	1216344	1216344
4.0	1.891853	298946	298946
5.0	1.957456	70010	70010
6.0	1.990658	15872	15872
7.0	2.007461	3466	3466
8.0	2.015965	782	782
9.0	2.020268	215	215
10.0	2.022446	68	68
11.0	2.023549	54	54
12.0	2.024107	24	24
13.0	2.024389	23	23
14.0	2.024532	21	21
15.0	2.024604	18	18
16.0	2.024641	21	21
17.0	2.024659	9	9
18.0	2.024669	14	14
19.0	2.024673	10	10
20.0	2.024676	5	5
21.0	2.024677	7	7
22.0	2.024678	10	10
23.0	2.024678	11	11
24.0	2.024678	8	8
25.0	2.024678	6	6
26.0	2.024678	7	7
27.0	2.024678	2	2
28.0	2.024678	6	6
29.0	2.024678	2	2
30.0	2.024678	7	7
31.0	2.024678	5	5
32.0	2.024678	5	5
33.0	2.024678	0	0
34.0	2.024678	2	2
35.0	2.024678	0	0
36.0	2.024678	5	5
37.0	2.024678	3	3
38.0	2.024678	2	2
39.0	2.024678	4	4
40.0	2.024678	2	2
41.0	2.024678	1	1
42.0	2.024678	5	5
43.0	2.024678	2	2
44.0	2.024678	0	0
45.0	2.024678	1	1
46.0	2.024678	1	1
47.0	2.024678	2	2
48.0	2.024678	2	2
49.0	2.024678	0	0
50.0	2.024678	2	2
51.0	2.024678	1	1
52.0	2.024678	0	0
53.0	2.024678	2	2
54.0	2.024678	0	0
55.0	2.024678	0	0
56.0	2.024678	1	1
57.0	2.024678	2	2
58.0	2.024678	1	1
59.0	2.024678	2	2
60.0	2.024678	1	1
61.0	2.024678	0	0
62.0	2.024678	0	0
63.0	2.024678	1	1
64.0	2.024678	0	0
65.0	2.024678	1	1
66.0	2.024678	0	0
67.0	2.024678	1	1
68.0	2.024678	0	0
69.0	2.024678	0	0
70.0	2.024678	1	1
71.0	2.024678	1	1
72.0	2.024678	0	0
73.0	2.024678	0	0
74.0	2.024678	0	0
75.0	2.024678	0	0
76.0	2.024678	1	1
77.0	2.024678	2	2
78.0	2.024678	0	0
79.0	2.024678	0	0
80.0	2.024678	0	0
81.0	2.024678	0	0
82.0	2.024678	0	0
83.0	2.024678	0	0
84.0	2.024678	0	0
85.0	2.024678	1	1
86.0	2.024678	0	0
87.0	2.024678	1	1
88.0	2.024678	1	1
89.0	2.024678	1	1
90.0	2.024678	0	0
91.0	2.024678	0	0
92.0	2.024678	0	0
93.0	2.024678	0	0
94.0	2.024678	0	0
95.0	2.024678	0	0
96.0	2.024678	1	1
97.0	2.024678	0	0
98.0	2.024678	1	1
99.0	2.024678	0	0
100.0	2.024678	0	0
102.0	0	1	1
103.0	0	1	1
108.0	0	1	1
109.0	0	1	1
111.0	0	1	1
112.0	0	1	1
117.0	0	1	1
121.0	0	1	1
125.0	0	1	1
154.0	0	1	1
162.0	0	1	1
174.0	0	1	1
204.0	0	1	1
227.0	0	1	1
367.0	0	1	1