## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-10-20/AT_Wie_Gro_1_2012-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-10-20/AT_Wie_Gro_1_2012-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-10-20/AT_Wie_Gro_1_2012-10-20.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 08:32:45 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	4983400	46172158	0	0	1788646	202144	0	0.022531	5257740374

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	45465433	45465433
2.0	1.991257	87643	87643
3.0	2.973847	8195	8195
4.0	3.947845	2052	2052
5.0	4.913328	769	769
6.0	5.870369	382	382
7.0	6.819043	213	213
8.0	7.759422	169	169
9.0	8.691579	149	149
10.0	9.615586	102	102
11.0	10.531514	110	110
12.0	11.439434	92	92
13.0	12.339415	83	83
14.0	13.231528	66	66
15.0	14.115841	43	43
16.0	14.992422	45	45
17.0	15.861338	51	51
18.0	16.722658	45	45
19.0	17.576447	34	34
20.0	18.422771	22	22
21.0	19.261695	41	41
22.0	20.093284	27	27
23.0	20.917602	25	25
24.0	21.734713	26	26
25.0	22.54468	19	19
26.0	23.347565	12	12
27.0	24.14343	14	14
28.0	24.932337	21	21
29.0	25.714346	13	13
30.0	26.489518	12	12
31.0	27.257912	14	14
32.0	28.019588	6	6
33.0	28.774604	13	13
34.0	29.523019	11	11
35.0	30.26489	12	12
36.0	31.000275	8	8
37.0	31.72923	4	4
38.0	32.451812	6	6
39.0	33.168076	7	7
40.0	33.878078	6	6
41.0	34.581871	6	6
42.0	35.279512	3	3
43.0	35.971052	3	3
44.0	36.656546	2	2
45.0	37.336047	7	7
46.0	38.009607	4	4
47.0	38.677277	4	4
48.0	39.33911	6	6
49.0	39.995156	0	0
50.0	40.645467	1	1
51.0	41.290091	3	3
52.0	41.929079	4	4
53.0	42.562481	4	4
54.0	43.190344	2	2
55.0	43.812718	0	0
56.0	44.42965	6	6
57.0	45.041188	1	1
58.0	45.647379	4	4
59.0	46.248271	2	2
60.0	46.843908	5	5
61.0	47.434337	5	5
62.0	48.019605	0	0
63.0	48.599755	2	2
64.0	49.174832	0	0
65.0	49.744882	4	4
66.0	50.309947	2	2
67.0	50.870072	5	5
68.0	51.4253	4	4
69.0	51.975673	0	0
70.0	52.521234	2	2
71.0	53.062025	2	2
72.0	53.598088	4	4
73.0	54.129463	3	3
74.0	54.656193	2	2
75.0	55.178317	2	2
76.0	55.695877	4	4
77.0	56.208911	4	4
78.0	56.717459	1	1
79.0	57.221561	1	1
80.0	57.721256	1	1
81.0	58.216582	1	1
82.0	58.707576	2	2
83.0	59.194278	1	1
84.0	59.676725	2	2
85.0	60.154953	1	1
86.0	60.629	2	2
87.0	61.098903	2	2
88.0	61.564696	0	0
89.0	62.026418	3	3
90.0	62.484102	2	2
91.0	62.937785	0	0
92.0	63.3875	0	0
93.0	63.833284	3	3
94.0	64.275171	0	0
95.0	64.713193	0	0
96.0	65.147386	1	1
97.0	65.577783	1	1
98.0	66.004417	1	1
99.0	66.42732	2	2
100.0	66.846526	1	1
101.0	0	2	2
103.0	0	3	3
105.0	0	2	2
109.0	0	2	2
110.0	0	3	3
112.0	0	2	2
113.0	0	2	2
114.0	0	1	1
115.0	0	3	3
118.0	0	1	1
119.0	0	2	2
120.0	0	1	1
121.0	0	2	2
127.0	0	1	1
128.0	0	2	2
129.0	0	1	1
131.0	0	1	1
133.0	0	1	1
134.0	0	3	3
136.0	0	1	1
137.0	0	1	1
140.0	0	1	1
143.0	0	2	2
144.0	0	1	1
146.0	0	1	1
149.0	0	1	1
150.0	0	1	1
154.0	0	3	3
155.0	0	1	1
156.0	0	1	1
157.0	0	1	1
161.0	0	1	1
167.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	2	2
175.0	0	2	2
177.0	0	1	1
182.0	0	1	1
186.0	0	1	1
189.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
198.0	0	3	3
204.0	0	1	1
210.0	0	1	1
211.0	0	2	2
213.0	0	1	1
214.0	0	1	1
216.0	0	1	1
219.0	0	1	1
220.0	0	2	2
234.0	0	1	1
240.0	0	1	1
265.0	0	1	1
270.0	0	1	1
272.0	0	1	1
277.0	0	1	1
281.0	0	1	1
301.0	0	1	1
312.0	0	1	1
316.0	0	1	1
321.0	0	1	1
322.0	0	1	1
330.0	0	1	1
334.0	0	1	1
335.0	0	1	1
341.0	0	1	1
370.0	0	1	1
396.0	0	1	1
415.0	0	1	1
416.0	0	1	1
417.0	0	1	1
425.0	0	1	1
428.0	0	1	1
477.0	0	1	1
486.0	0	1	1
494.0	0	1	1
512.0	0	1	1
543.0	0	1	1
545.0	0	1	1
548.0	0	1	1
580.0	0	1	1
608.0	0	1	1
618.0	0	1	1
631.0	0	1	1
632.0	0	1	1
633.0	0	2	2
681.0	0	2	2
691.0	0	1	1
724.0	0	1	1
731.0	0	1	1
742.0	0	1	1
786.0	0	1	1
787.0	0	1	1
845.0	0	1	1
1104.0	0	1	1
1225.0	0	1	1
1430.0	0	1	1
1450.0	0	1	1
1798.0	0	1	1
1836.0	0	1	1
2761.0	0	1	1
12114.0	0	1	1