## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-06-30/RS_Zaj_Kal_1_2016-06-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-06-30/RS_Zaj_Kal_1_2016-06-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-06-30/RS_Zaj_Kal_1_2016-06-30.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 08:55:35 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	32229269	10692096	0	0	7606254	927612	0	0.176476	58002987

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8836492	8836492
2.0	1.831655	571066	571066
3.0	2.523306	44615	44615
4.0	3.098522	5785	5785
5.0	3.576903	2073	2073
6.0	3.974751	1288	1288
7.0	4.305623	832	832
8.0	4.580795	629	629
9.0	4.809644	465	465
10.0	4.999966	358	358
11.0	5.15825	293	293
12.0	5.289887	259	259
13.0	5.399363	185	185
14.0	5.49041	173	173
15.0	5.56613	160	160
16.0	5.629102	155	155
17.0	5.681474	137	137
18.0	5.725029	112	112
19.0	5.761252	109	109
20.0	5.791377	119	119
21.0	5.81643	92	92
22.0	5.837266	89	89
23.0	5.854595	97	97
24.0	5.869006	92	92
25.0	5.880991	109	109
26.0	5.890958	93	93
27.0	5.899248	89	89
28.0	5.906142	72	72
29.0	5.911875	75	75
30.0	5.916644	77	77
31.0	5.920609	54	54
32.0	5.923907	50	50
33.0	5.92665	63	63
34.0	5.928931	62	62
35.0	5.930828	53	53
36.0	5.932406	49	49
37.0	5.933718	39	39
38.0	5.934809	48	48
39.0	5.935717	45	45
40.0	5.936471	38	38
41.0	5.937099	30	30
42.0	5.937621	42	42
43.0	5.938055	37	37
44.0	5.938416	32	32
45.0	5.938717	27	27
46.0	5.938966	25	25
47.0	5.939174	26	26
48.0	5.939347	31	31
49.0	5.93949	23	23
50.0	5.93961	24	24
51.0	5.939709	13	13
52.0	5.939792	23	23
53.0	5.93986	17	17
54.0	5.939918	19	19
55.0	5.939965	20	20
56.0	5.940005	13	13
57.0	5.940038	15	15
58.0	5.940065	14	14
59.0	5.940088	24	24
60.0	5.940106	14	14
61.0	5.940122	21	21
62.0	5.940135	11	11
63.0	5.940146	13	13
64.0	5.940155	15	15
65.0	5.940163	12	12
66.0	5.940169	8	8
67.0	5.940174	8	8
68.0	5.940179	15	15
69.0	5.940182	7	7
70.0	5.940185	4	4
71.0	5.940188	11	11
72.0	5.94019	3	3
73.0	5.940191	17	17
74.0	5.940193	12	12
75.0	5.940194	11	11
76.0	5.940195	10	10
77.0	5.940196	7	7
78.0	5.940197	13	13
79.0	5.940197	8	8
80.0	5.940198	14	14
81.0	5.940198	9	9
82.0	5.940198	11	11
83.0	5.940199	8	8
84.0	5.940199	8	8
85.0	5.940199	4	4
86.0	5.940199	12	12
87.0	5.940199	7	7
88.0	5.940199	13	13
89.0	5.940199	12	12
90.0	5.9402	9	9
91.0	5.9402	10	10
92.0	5.9402	10	10
93.0	5.9402	8	8
94.0	5.9402	11	11
95.0	5.9402	12	12
96.0	5.9402	8	8
97.0	5.9402	10	10
98.0	5.9402	10	10
99.0	5.9402	9	9
100.0	5.9402	8	8
101.0	0	5	5
102.0	0	4	4
103.0	0	6	6
104.0	0	8	8
105.0	0	10	10
106.0	0	9	9
107.0	0	3	3
108.0	0	6	6
109.0	0	12	12
110.0	0	2	2
111.0	0	6	6
112.0	0	7	7
113.0	0	8	8
114.0	0	6	6
115.0	0	9	9
116.0	0	7	7
117.0	0	7	7
118.0	0	8	8
119.0	0	11	11
120.0	0	7	7
121.0	0	4	4
122.0	0	4	4
123.0	0	7	7
125.0	0	5	5
126.0	0	5	5
128.0	0	5	5
129.0	0	1	1
130.0	0	3	3
131.0	0	6	6
132.0	0	7	7
133.0	0	4	4
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	1	1
138.0	0	2	2
139.0	0	2	2
140.0	0	2	2
141.0	0	5	5
142.0	0	4	4
143.0	0	3	3
144.0	0	7	7
145.0	0	4	4
146.0	0	5	5
147.0	0	4	4
148.0	0	4	4
149.0	0	3	3
150.0	0	1	1
151.0	0	5	5
152.0	0	1	1
153.0	0	6	6
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	5	5
160.0	0	3	3
161.0	0	5	5
162.0	0	2	2
164.0	0	2	2
165.0	0	1	1
166.0	0	1	1
167.0	0	3	3
168.0	0	1	1
169.0	0	1	1
170.0	0	3	3
171.0	0	1	1
172.0	0	1	1
173.0	0	7	7
175.0	0	3	3
176.0	0	3	3
177.0	0	3	3
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
182.0	0	1	1
183.0	0	1	1
184.0	0	4	4
185.0	0	2	2
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	3	3
192.0	0	1	1
193.0	0	2	2
194.0	0	3	3
198.0	0	2	2
199.0	0	2	2
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	4	4
205.0	0	3	3
206.0	0	4	4
207.0	0	1	1
208.0	0	2	2
209.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	2	2
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
225.0	0	2	2
226.0	0	1	1
227.0	0	1	1
228.0	0	2	2
230.0	0	1	1
231.0	0	3	3
235.0	0	1	1
236.0	0	3	3
237.0	0	1	1
240.0	0	2	2
242.0	0	1	1
243.0	0	1	1
246.0	0	1	1
248.0	0	1	1
249.0	0	1	1
254.0	0	1	1
256.0	0	1	1
257.0	0	1	1
261.0	0	2	2
263.0	0	1	1
264.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	2	2
273.0	0	1	1
279.0	0	1	1
281.0	0	1	1
286.0	0	1	1
289.0	0	2	2
291.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	2	2
315.0	0	1	1
321.0	0	1	1
323.0	0	1	1
325.0	0	1	1
328.0	0	2	2
329.0	0	1	1
333.0	0	1	1
337.0	0	1	1
343.0	0	1	1
349.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	3	3
359.0	0	2	2
362.0	0	1	1
366.0	0	2	2
367.0	0	1	1
369.0	0	1	1
374.0	0	1	1
375.0	0	1	1
382.0	0	1	1
394.0	0	2	2
397.0	0	1	1
400.0	0	1	1
406.0	0	1	1
408.0	0	1	1
409.0	0	1	1
413.0	0	1	1
420.0	0	1	1
436.0	0	1	1
439.0	0	1	1
443.0	0	1	1
446.0	0	1	1
449.0	0	1	1
470.0	0	1	1
471.0	0	1	1
475.0	0	2	2
486.0	0	1	1
490.0	0	1	1
492.0	0	1	1
519.0	0	1	1
530.0	0	1	1
531.0	0	1	1
536.0	0	1	1
539.0	0	1	1
587.0	0	1	1
624.0	0	1	1
704.0	0	1	1
746.0	0	1	1
810.0	0	1	1
827.0	0	1	1
932.0	0	1	1
937.0	0	1	1
1138.0	0	1	1
1284.0	0	1	1
1295.0	0	1	1
1355.0	0	1	1
1429.0	0	1	1
2006.0	0	1	1
3227.0	0	1	1