## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-06-01/DE_Bay_Mun_1_2015-06-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-06-01/DE_Bay_Mun_1_2015-06-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2015-06-01/DE_Bay_Mun_1_2015-06-01.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 08:36:53 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	6259769	31393178	0	0	2666100	6836375	0	0.236637	61184038

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18891180	18891180
2.0	1.59864	4306686	4306686
3.0	1.957011	896706	896706
4.0	2.171546	175792	175792
5.0	2.299975	32870	32870
6.0	2.376858	6334	6334
7.0	2.422883	1320	1320
8.0	2.450436	403	403
9.0	2.46693	220	220
10.0	2.476804	179	179
11.0	2.482715	158	158
12.0	2.486253	102	102
13.0	2.488372	104	104
14.0	2.48964	107	107
15.0	2.490399	61	61
16.0	2.490853	67	67
17.0	2.491125	65	65
18.0	2.491288	56	56
19.0	2.491386	61	61
20.0	2.491444	46	46
21.0	2.491479	40	40
22.0	2.4915	46	46
23.0	2.491512	28	28
24.0	2.49152	19	19
25.0	2.491524	29	29
26.0	2.491527	31	31
27.0	2.491529	30	30
28.0	2.49153	18	18
29.0	2.49153	23	23
30.0	2.491531	14	14
31.0	2.491531	25	25
32.0	2.491531	16	16
33.0	2.491531	12	12
34.0	2.491531	9	9
35.0	2.491531	15	15
36.0	2.491531	12	12
37.0	2.491531	15	15
38.0	2.491531	8	8
39.0	2.491531	5	5
40.0	2.491531	7	7
41.0	2.491531	13	13
42.0	2.491531	6	6
43.0	2.491531	12	12
44.0	2.491531	6	6
45.0	2.491531	4	4
46.0	2.491531	5	5
47.0	2.491531	3	3
48.0	2.491531	3	3
49.0	2.491531	2	2
50.0	2.491531	3	3
51.0	2.491531	1	1
52.0	2.491531	3	3
53.0	2.491531	11	11
54.0	2.491531	3	3
55.0	2.491531	4	4
56.0	2.491531	4	4
57.0	2.491531	2	2
58.0	2.491531	4	4
59.0	2.491531	2	2
60.0	2.491531	4	4
61.0	2.491531	3	3
62.0	2.491531	2	2
63.0	2.491531	5	5
64.0	2.491531	1	1
65.0	2.491531	4	4
66.0	2.491531	5	5
67.0	2.491531	2	2
68.0	2.491531	2	2
69.0	2.491531	2	2
70.0	2.491531	1	1
71.0	2.491531	2	2
72.0	2.491531	1	1
73.0	2.491531	0	0
74.0	2.491531	0	0
75.0	2.491531	0	0
76.0	2.491531	1	1
77.0	2.491531	0	0
78.0	2.491531	0	0
79.0	2.491531	2	2
80.0	2.491531	1	1
81.0	2.491531	1	1
82.0	2.491531	1	1
83.0	2.491531	3	3
84.0	2.491531	0	0
85.0	2.491531	1	1
86.0	2.491531	3	3
87.0	2.491531	3	3
88.0	2.491531	0	0
89.0	2.491531	0	0
90.0	2.491531	0	0
91.0	2.491531	0	0
92.0	2.491531	0	0
93.0	2.491531	1	1
94.0	2.491531	0	0
95.0	2.491531	0	0
96.0	2.491531	0	0
97.0	2.491531	1	1
98.0	2.491531	1	1
99.0	2.491531	1	1
100.0	2.491531	1	1
102.0	0	3	3
103.0	0	1	1
109.0	0	1	1
110.0	0	1	1
114.0	0	1	1
124.0	0	1	1
136.0	0	1	1
159.0	0	1	1
316.0	0	1	1