## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Sre_Sla_1_2016-06-18/RS_Sre_Sla_1_2016-06-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Sre_Sla_1_2016-06-18/RS_Sre_Sla_1_2016-06-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Sre_Sla_1_2016-06-18/RS_Sre_Sla_1_2016-06-18.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 08:41:13 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	30457345	9256098	0	0	6517167	804728	0	0.165953	50100215

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	7645398	7645398
2.0	1.831311	509343	509343
3.0	2.522388	41028	41028
4.0	3.096888	5253	5253
5.0	3.574476	1691	1691
6.0	3.9715	1036	1036
7.0	4.301551	685	685
8.0	4.575925	442	442
9.0	4.804016	332	332
10.0	4.99363	264	264
11.0	5.151258	226	226
12.0	5.282296	193	193
13.0	5.391229	172	172
14.0	5.481786	170	170
15.0	5.557068	121	121
16.0	5.61965	118	118
17.0	5.671675	95	95
18.0	5.714924	107	107
19.0	5.750878	92	92
20.0	5.780766	90	90
21.0	5.805613	79	79
22.0	5.826268	86	86
23.0	5.843439	99	99
24.0	5.857713	81	81
25.0	5.86958	73	73
26.0	5.879445	67	67
27.0	5.887645	76	76
28.0	5.894462	69	69
29.0	5.90013	61	61
30.0	5.904841	56	56
31.0	5.908758	63	63
32.0	5.912013	44	44
33.0	5.91472	55	55
34.0	5.91697	44	44
35.0	5.918841	47	47
36.0	5.920395	50	50
37.0	5.921688	43	43
38.0	5.922763	42	42
39.0	5.923656	25	25
40.0	5.924399	39	39
41.0	5.925016	43	43
42.0	5.925529	30	30
43.0	5.925956	35	35
44.0	5.926311	23	23
45.0	5.926605	25	25
46.0	5.926851	20	20
47.0	5.927054	23	23
48.0	5.927224	21	21
49.0	5.927364	21	21
50.0	5.927482	14	14
51.0	5.927579	19	19
52.0	5.92766	14	14
53.0	5.927727	18	18
54.0	5.927783	21	21
55.0	5.927829	16	16
56.0	5.927868	15	15
57.0	5.9279	17	17
58.0	5.927927	7	7
59.0	5.927949	11	11
60.0	5.927967	12	12
61.0	5.927983	14	14
62.0	5.927996	12	12
63.0	5.928006	10	10
64.0	5.928015	8	8
65.0	5.928022	9	9
66.0	5.928028	16	16
67.0	5.928033	7	7
68.0	5.928038	17	17
69.0	5.928041	7	7
70.0	5.928044	12	12
71.0	5.928046	15	15
72.0	5.928049	14	14
73.0	5.92805	14	14
74.0	5.928052	12	12
75.0	5.928053	13	13
76.0	5.928054	10	10
77.0	5.928054	9	9
78.0	5.928055	6	6
79.0	5.928056	8	8
80.0	5.928056	7	7
81.0	5.928057	8	8
82.0	5.928057	7	7
83.0	5.928057	10	10
84.0	5.928057	6	6
85.0	5.928058	14	14
86.0	5.928058	7	7
87.0	5.928058	8	8
88.0	5.928058	5	5
89.0	5.928058	6	6
90.0	5.928058	14	14
91.0	5.928058	11	11
92.0	5.928058	7	7
93.0	5.928058	7	7
94.0	5.928058	8	8
95.0	5.928058	4	4
96.0	5.928058	10	10
97.0	5.928058	6	6
98.0	5.928058	12	12
99.0	5.928058	6	6
100.0	5.928058	10	10
101.0	0	9	9
102.0	0	9	9
103.0	0	7	7
104.0	0	13	13
105.0	0	6	6
106.0	0	9	9
107.0	0	6	6
108.0	0	9	9
109.0	0	2	2
110.0	0	5	5
111.0	0	7	7
112.0	0	8	8
113.0	0	6	6
114.0	0	7	7
115.0	0	7	7
116.0	0	5	5
117.0	0	6	6
118.0	0	5	5
119.0	0	3	3
120.0	0	6	6
121.0	0	2	2
122.0	0	1	1
123.0	0	6	6
124.0	0	3	3
125.0	0	4	4
126.0	0	5	5
127.0	0	2	2
128.0	0	4	4
129.0	0	4	4
130.0	0	2	2
131.0	0	3	3
132.0	0	6	6
133.0	0	3	3
134.0	0	2	2
135.0	0	3	3
136.0	0	2	2
137.0	0	3	3
138.0	0	5	5
139.0	0	1	1
140.0	0	3	3
141.0	0	4	4
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
146.0	0	5	5
147.0	0	3	3
148.0	0	2	2
149.0	0	1	1
150.0	0	4	4
151.0	0	2	2
152.0	0	3	3
153.0	0	7	7
154.0	0	4	4
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
159.0	0	1	1
160.0	0	3	3
162.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
166.0	0	3	3
167.0	0	3	3
168.0	0	1	1
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	3	3
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
177.0	0	2	2
178.0	0	3	3
179.0	0	2	2
180.0	0	2	2
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
187.0	0	4	4
188.0	0	1	1
189.0	0	1	1
193.0	0	1	1
197.0	0	2	2
198.0	0	1	1
199.0	0	2	2
200.0	0	2	2
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
208.0	0	4	4
209.0	0	1	1
210.0	0	1	1
213.0	0	1	1
214.0	0	1	1
218.0	0	1	1
219.0	0	1	1
222.0	0	1	1
223.0	0	1	1
226.0	0	1	1
228.0	0	2	2
229.0	0	1	1
232.0	0	1	1
234.0	0	1	1
235.0	0	1	1
240.0	0	1	1
245.0	0	3	3
248.0	0	1	1
253.0	0	1	1
254.0	0	2	2
256.0	0	2	2
257.0	0	1	1
258.0	0	1	1
266.0	0	1	1
278.0	0	1	1
280.0	0	1	1
282.0	0	1	1
284.0	0	1	1
288.0	0	1	1
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
297.0	0	1	1
301.0	0	1	1
304.0	0	1	1
312.0	0	1	1
318.0	0	2	2
322.0	0	2	2
323.0	0	2	2
324.0	0	1	1
325.0	0	1	1
340.0	0	1	1
345.0	0	1	1
350.0	0	1	1
358.0	0	1	1
365.0	0	1	1
366.0	0	1	1
372.0	0	1	1
374.0	0	1	1
377.0	0	1	1
379.0	0	1	1
389.0	0	1	1
392.0	0	1	1
398.0	0	1	1
407.0	0	1	1
411.0	0	1	1
414.0	0	1	1
426.0	0	1	1
430.0	0	1	1
432.0	0	1	1
440.0	0	2	2
442.0	0	1	1
456.0	0	1	1
460.0	0	1	1
461.0	0	1	1
466.0	0	1	1
477.0	0	1	1
491.0	0	1	1
495.0	0	1	1
532.0	0	1	1
545.0	0	1	1
592.0	0	1	1
601.0	0	1	1
672.0	0	1	1
695.0	0	1	1
727.0	0	1	1
933.0	0	1	1
1450.0	0	1	1