## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-10-23/TR_Ank_Yes_1_2014-10-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-10-23/TR_Ank_Yes_1_2014-10-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-10-23/TR_Ank_Yes_1_2014-10-23.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 08:46:59 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	2886091	20546142	0	0	710380	829100	0	0.053858	247683841

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18543613	18543613
2.0	1.920394	625325	625325
3.0	2.76752	19779	19779
4.0	3.54721	1252	1252
5.0	4.264832	494	494
6.0	4.925327	286	286
7.0	5.533243	237	237
8.0	6.092765	197	197
9.0	6.607746	158	158
10.0	7.081732	144	144
11.0	7.517986	117	117
12.0	7.919512	102	102
13.0	8.289073	90	90
14.0	8.629216	89	89
15.0	8.942281	60	60
16.0	9.230425	53	53
17.0	9.495631	67	67
18.0	9.739725	70	70
19.0	9.964387	63	63
20.0	10.171165	58	58
21.0	10.361483	48	48
22.0	10.53665	39	39
23.0	10.697872	41	41
24.0	10.846261	45	45
25.0	10.982837	33	33
26.0	11.108541	38	38
27.0	11.224238	35	35
28.0	11.330725	32	32
29.0	11.428734	34	34
30.0	11.518942	26	26
31.0	11.601969	29	29
32.0	11.678386	30	30
33.0	11.74872	23	23
34.0	11.813455	12	12
35.0	11.873037	22	22
36.0	11.927876	16	16
37.0	11.978349	24	24
38.0	12.024804	21	21
39.0	12.067562	24	24
40.0	12.106915	18	18
41.0	12.143136	13	13
42.0	12.176473	21	21
43.0	12.207157	11	11
44.0	12.235398	16	16
45.0	12.26139	16	16
46.0	12.285314	20	20
47.0	12.307333	22	22
48.0	12.327599	20	20
49.0	12.346252	11	11
50.0	12.363421	11	11
51.0	12.379222	20	20
52.0	12.393766	13	13
53.0	12.407151	10	10
54.0	12.419472	8	8
55.0	12.430811	13	13
56.0	12.441248	10	10
57.0	12.450854	12	12
58.0	12.459695	14	14
59.0	12.467832	8	8
60.0	12.475322	16	16
61.0	12.482215	13	13
62.0	12.48856	7	7
63.0	12.4944	8	8
64.0	12.499775	10	10
65.0	12.504721	9	9
66.0	12.509274	11	11
67.0	12.513465	11	11
68.0	12.517322	10	10
69.0	12.520872	9	9
70.0	12.52414	2	2
71.0	12.527147	6	6
72.0	12.529915	6	6
73.0	12.532462	6	6
74.0	12.534807	11	11
75.0	12.536965	8	8
76.0	12.538951	5	5
77.0	12.54078	4	4
78.0	12.542462	5	5
79.0	12.544011	4	4
80.0	12.545436	11	11
81.0	12.546748	6	6
82.0	12.547956	2	2
83.0	12.549067	9	9
84.0	12.55009	4	4
85.0	12.551032	3	3
86.0	12.551898	8	8
87.0	12.552696	7	7
88.0	12.55343	7	7
89.0	12.554105	5	5
90.0	12.554727	6	6
91.0	12.555299	5	5
92.0	12.555826	4	4
93.0	12.556311	7	7
94.0	12.556757	3	3
95.0	12.557168	11	11
96.0	12.557546	6	6
97.0	12.557894	5	5
98.0	12.558214	5	5
99.0	12.558509	5	5
100.0	12.55878	5	5
101.0	0	6	6
102.0	0	5	5
103.0	0	2	2
104.0	0	4	4
105.0	0	4	4
106.0	0	5	5
107.0	0	5	5
108.0	0	3	3
109.0	0	6	6
110.0	0	5	5
111.0	0	7	7
112.0	0	3	3
113.0	0	2	2
114.0	0	5	5
115.0	0	4	4
116.0	0	1	1
117.0	0	2	2
118.0	0	3	3
119.0	0	3	3
120.0	0	2	2
121.0	0	4	4
122.0	0	7	7
123.0	0	3	3
124.0	0	4	4
125.0	0	2	2
126.0	0	2	2
127.0	0	3	3
128.0	0	1	1
129.0	0	3	3
130.0	0	3	3
131.0	0	4	4
132.0	0	5	5
133.0	0	2	2
135.0	0	2	2
136.0	0	5	5
137.0	0	5	5
138.0	0	3	3
139.0	0	2	2
140.0	0	3	3
141.0	0	1	1
142.0	0	1	1
143.0	0	4	4
144.0	0	2	2
145.0	0	3	3
147.0	0	4	4
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	2	2
154.0	0	2	2
155.0	0	4	4
156.0	0	4	4
157.0	0	2	2
159.0	0	3	3
160.0	0	1	1
161.0	0	2	2
162.0	0	1	1
163.0	0	2	2
164.0	0	1	1
166.0	0	4	4
167.0	0	5	5
168.0	0	6	6
169.0	0	1	1
171.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	3	3
176.0	0	2	2
177.0	0	2	2
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
182.0	0	2	2
184.0	0	2	2
185.0	0	1	1
189.0	0	1	1
190.0	0	4	4
191.0	0	2	2
192.0	0	1	1
193.0	0	2	2
194.0	0	1	1
195.0	0	3	3
196.0	0	1	1
197.0	0	2	2
199.0	0	3	3
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
209.0	0	1	1
210.0	0	3	3
211.0	0	3	3
212.0	0	3	3
213.0	0	4	4
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	1	1
224.0	0	4	4
226.0	0	1	1
228.0	0	2	2
229.0	0	2	2
230.0	0	1	1
232.0	0	2	2
233.0	0	1	1
235.0	0	3	3
237.0	0	1	1
239.0	0	2	2
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
247.0	0	2	2
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
256.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
262.0	0	1	1
264.0	0	1	1
265.0	0	2	2
267.0	0	1	1
269.0	0	3	3
273.0	0	1	1
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
282.0	0	2	2
284.0	0	3	3
285.0	0	1	1
288.0	0	1	1
295.0	0	1	1
299.0	0	1	1
301.0	0	1	1
306.0	0	1	1
307.0	0	1	1
308.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	2	2
316.0	0	1	1
320.0	0	2	2
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
338.0	0	2	2
339.0	0	1	1
345.0	0	2	2
350.0	0	1	1
355.0	0	1	1
360.0	0	1	1
361.0	0	1	1
362.0	0	1	1
365.0	0	1	1
367.0	0	1	1
368.0	0	2	2
376.0	0	1	1
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
388.0	0	1	1
396.0	0	1	1
401.0	0	1	1
407.0	0	1	1
408.0	0	1	1
416.0	0	2	2
419.0	0	1	1
435.0	0	1	1
439.0	0	1	1
447.0	0	1	1
448.0	0	1	1
467.0	0	1	1
468.0	0	1	1
481.0	0	1	1
488.0	0	1	1
490.0	0	1	1
491.0	0	1	1
492.0	0	1	1
501.0	0	2	2
502.0	0	2	2
510.0	0	1	1
522.0	0	1	1
523.0	0	1	1
528.0	0	1	1
531.0	0	1	1
546.0	0	1	1
550.0	0	2	2
566.0	0	1	1
577.0	0	1	1
595.0	0	1	1
598.0	0	1	1
606.0	0	1	1
634.0	0	1	1
636.0	0	1	1
650.0	0	1	1
679.0	0	1	1
687.0	0	1	1
696.0	0	1	1
746.0	0	1	1
761.0	0	1	1
833.0	0	1	1
968.0	0	1	1
1139.0	0	1	1