## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-08-24/TR_Ank_Yes_1_2016-08-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-08-24/TR_Ank_Yes_1_2016-08-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-08-24/TR_Ank_Yes_1_2016-08-24.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 08:46:16 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	27491348	10198749	0	0	6158151	866215	0	0.164769	56589626

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8447878	8447878
2.0	1.835084	570691	570691
3.0	2.532449	45375	45375
4.0	3.114808	5776	5776
5.0	3.601126	1903	1903
6.0	4.007243	1052	1052
7.0	4.346385	687	687
8.0	4.629596	501	501
9.0	4.866102	377	377
10.0	5.063604	305	305
11.0	5.228535	256	256
12.0	5.366266	192	192
13.0	5.481283	209	209
14.0	5.577332	184	184
15.0	5.65754	154	154
16.0	5.724522	129	129
17.0	5.780456	131	131
18.0	5.827167	98	98
19.0	5.866174	124	124
20.0	5.898748	106	106
21.0	5.92595	113	113
22.0	5.948666	87	87
23.0	5.967636	104	104
24.0	5.983477	85	85
25.0	5.996706	80	80
26.0	6.007754	58	58
27.0	6.016979	75	75
28.0	6.024683	69	69
29.0	6.031116	67	67
30.0	6.036489	61	61
31.0	6.040975	55	55
32.0	6.044722	39	39
33.0	6.047851	36	36
34.0	6.050463	47	47
35.0	6.052645	49	49
36.0	6.054467	42	42
37.0	6.055989	46	46
38.0	6.057259	33	33
39.0	6.058321	31	31
40.0	6.059207	37	37
41.0	6.059947	25	25
42.0	6.060565	24	24
43.0	6.061081	27	27
44.0	6.061511	21	21
45.0	6.061871	23	23
46.0	6.062172	17	17
47.0	6.062423	24	24
48.0	6.062632	16	16
49.0	6.062807	25	25
50.0	6.062954	29	29
51.0	6.063076	17	17
52.0	6.063177	18	18
53.0	6.063263	18	18
54.0	6.063334	16	16
55.0	6.063393	15	15
56.0	6.063443	15	15
57.0	6.063484	17	17
58.0	6.063519	14	14
59.0	6.063547	10	10
60.0	6.063571	18	18
61.0	6.063592	12	12
62.0	6.063608	6	6
63.0	6.063622	3	3
64.0	6.063634	10	10
65.0	6.063644	6	6
66.0	6.063652	12	12
67.0	6.063659	13	13
68.0	6.063665	9	9
69.0	6.063669	7	7
70.0	6.063673	17	17
71.0	6.063677	7	7
72.0	6.063679	12	12
73.0	6.063682	16	16
74.0	6.063684	11	11
75.0	6.063685	17	17
76.0	6.063687	9	9
77.0	6.063688	8	8
78.0	6.063689	14	14
79.0	6.06369	11	11
80.0	6.06369	9	9
81.0	6.063691	13	13
82.0	6.063691	16	16
83.0	6.063692	11	11
84.0	6.063692	8	8
85.0	6.063692	8	8
86.0	6.063692	6	6
87.0	6.063693	7	7
88.0	6.063693	10	10
89.0	6.063693	7	7
90.0	6.063693	11	11
91.0	6.063693	10	10
92.0	6.063693	11	11
93.0	6.063693	7	7
94.0	6.063693	5	5
95.0	6.063693	6	6
96.0	6.063693	6	6
97.0	6.063693	7	7
98.0	6.063693	3	3
99.0	6.063693	5	5
100.0	6.063693	8	8
101.0	0	2	2
103.0	0	8	8
104.0	0	6	6
105.0	0	5	5
106.0	0	4	4
107.0	0	9	9
108.0	0	7	7
109.0	0	9	9
110.0	0	5	5
111.0	0	6	6
112.0	0	8	8
113.0	0	6	6
114.0	0	6	6
115.0	0	4	4
116.0	0	4	4
117.0	0	3	3
118.0	0	2	2
119.0	0	3	3
120.0	0	4	4
121.0	0	2	2
122.0	0	7	7
123.0	0	2	2
124.0	0	4	4
125.0	0	4	4
126.0	0	2	2
127.0	0	3	3
128.0	0	2	2
129.0	0	3	3
130.0	0	4	4
131.0	0	2	2
132.0	0	2	2
133.0	0	4	4
134.0	0	1	1
135.0	0	3	3
136.0	0	2	2
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
140.0	0	1	1
141.0	0	3	3
143.0	0	2	2
145.0	0	2	2
146.0	0	2	2
147.0	0	3	3
148.0	0	4	4
149.0	0	1	1
150.0	0	1	1
152.0	0	1	1
153.0	0	2	2
154.0	0	1	1
155.0	0	1	1
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	3	3
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	3	3
169.0	0	2	2
170.0	0	4	4
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
175.0	0	1	1
176.0	0	3	3
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	3	3
185.0	0	1	1
186.0	0	2	2
188.0	0	1	1
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	2	2
198.0	0	2	2
200.0	0	1	1
202.0	0	1	1
203.0	0	2	2
206.0	0	1	1
213.0	0	1	1
216.0	0	1	1
225.0	0	2	2
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
234.0	0	1	1
236.0	0	1	1
238.0	0	3	3
241.0	0	1	1
247.0	0	1	1
250.0	0	1	1
252.0	0	2	2
260.0	0	2	2
265.0	0	1	1
266.0	0	1	1
270.0	0	1	1
272.0	0	1	1
276.0	0	2	2
281.0	0	1	1
283.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	2	2
302.0	0	1	1
303.0	0	1	1
307.0	0	1	1
309.0	0	2	2
310.0	0	1	1
320.0	0	1	1
323.0	0	1	1
326.0	0	1	1
331.0	0	1	1
333.0	0	1	1
336.0	0	1	1
339.0	0	1	1
341.0	0	1	1
345.0	0	1	1
347.0	0	1	1
348.0	0	1	1
361.0	0	1	1
362.0	0	1	1
364.0	0	1	1
371.0	0	1	1
372.0	0	1	1
390.0	0	1	1
396.0	0	1	1
400.0	0	1	1
410.0	0	1	1
423.0	0	1	1
452.0	0	1	1
486.0	0	1	1
506.0	0	2	2
581.0	0	1	1
624.0	0	1	1
654.0	0	1	1
678.0	0	1	1
772.0	0	1	1
784.0	0	1	1
789.0	0	1	1
1169.0	0	1	1
1961.0	0	1	1