## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-05-21/FR_Dro_Got_1_2015-05-21.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-05-21/FR_Dro_Got_1_2015-05-21.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-05-21/FR_Dro_Got_1_2015-05-21.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 08:44:36 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	7877211	32094718	0	0	3312354	4756055	0	0.177953	97304810

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22918195	22918195
2.0	1.719041	3468921	3468921
3.0	2.236061	484426	484426
4.0	2.607819	66566	66566
5.0	2.875129	9686	9686
6.0	3.067336	1840	1840
7.0	3.20554	680	680
8.0	3.304915	377	377
9.0	3.376369	279	279
10.0	3.427748	244	244
11.0	3.464691	182	182
12.0	3.491255	164	164
13.0	3.510355	156	156
14.0	3.524089	117	117
15.0	3.533965	119	119
16.0	3.541066	112	112
17.0	3.546171	87	87
18.0	3.549843	84	84
19.0	3.552482	67	67
20.0	3.55438	56	56
21.0	3.555745	64	64
22.0	3.556727	63	63
23.0	3.557432	49	49
24.0	3.55794	51	51
25.0	3.558304	37	37
26.0	3.558567	44	44
27.0	3.558755	31	31
28.0	3.558891	29	29
29.0	3.558988	34	34
30.0	3.559059	24	24
31.0	3.559109	32	32
32.0	3.559145	22	22
33.0	3.559171	21	21
34.0	3.55919	23	23
35.0	3.559204	20	20
36.0	3.559213	18	18
37.0	3.55922	18	18
38.0	3.559225	21	21
39.0	3.559229	25	25
40.0	3.559231	15	15
41.0	3.559233	8	8
42.0	3.559235	9	9
43.0	3.559236	14	14
44.0	3.559236	14	14
45.0	3.559237	7	7
46.0	3.559237	5	5
47.0	3.559237	12	12
48.0	3.559238	11	11
49.0	3.559238	13	13
50.0	3.559238	11	11
51.0	3.559238	12	12
52.0	3.559238	4	4
53.0	3.559238	6	6
54.0	3.559238	8	8
55.0	3.559238	5	5
56.0	3.559238	5	5
57.0	3.559238	9	9
58.0	3.559238	5	5
59.0	3.559238	2	2
60.0	3.559238	7	7
61.0	3.559238	3	3
62.0	3.559238	6	6
63.0	3.559238	8	8
64.0	3.559238	4	4
65.0	3.559238	1	1
66.0	3.559238	4	4
67.0	3.559238	6	6
68.0	3.559238	8	8
69.0	3.559238	7	7
70.0	3.559238	7	7
71.0	3.559238	2	2
72.0	3.559238	4	4
73.0	3.559238	8	8
74.0	3.559238	2	2
75.0	3.559238	0	0
76.0	3.559238	2	2
77.0	3.559238	2	2
78.0	3.559238	2	2
79.0	3.559238	1	1
80.0	3.559238	3	3
81.0	3.559238	2	2
82.0	3.559238	2	2
83.0	3.559238	3	3
84.0	3.559238	2	2
85.0	3.559238	3	3
86.0	3.559238	5	5
87.0	3.559238	3	3
88.0	3.559238	5	5
89.0	3.559238	2	2
90.0	3.559238	0	0
91.0	3.559238	1	1
92.0	3.559238	1	1
93.0	3.559238	1	1
94.0	3.559238	2	2
95.0	3.559238	3	3
96.0	3.559238	2	2
97.0	3.559238	4	4
98.0	3.559238	1	1
99.0	3.559238	3	3
100.0	3.559238	2	2
101.0	0	3	3
102.0	0	1	1
103.0	0	1	1
104.0	0	1	1
105.0	0	1	1
108.0	0	3	3
110.0	0	1	1
111.0	0	2	2
112.0	0	1	1
113.0	0	1	1
114.0	0	3	3
116.0	0	1	1
117.0	0	1	1
119.0	0	5	5
120.0	0	2	2
122.0	0	1	1
124.0	0	1	1
127.0	0	1	1
128.0	0	2	2
131.0	0	1	1
133.0	0	1	1
134.0	0	2	2
140.0	0	2	2
142.0	0	1	1
143.0	0	1	1
145.0	0	1	1
146.0	0	1	1
161.0	0	1	1
166.0	0	1	1
172.0	0	1	1
175.0	0	1	1
188.0	0	1	1
190.0	0	2	2
193.0	0	1	1
197.0	0	1	1
211.0	0	1	1
216.0	0	1	1
221.0	0	1	1
232.0	0	1	1
252.0	0	1	1
264.0	0	2	2
321.0	0	1	1
383.0	0	1	1