## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-09-13/RS_Zaj_Kal_1_2016-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-09-13/RS_Zaj_Kal_1_2016-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RS_Zaj_Kal_1_2016-09-13/RS_Zaj_Kal_1_2016-09-13.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 09:16:47 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	40296432	11836379	0	0	10067946	964068	0	0.187529	68659301

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9910738	9910738
2.0	1.841648	615694	615694
3.0	2.55002	46382	46382
4.0	3.146221	5753	5753
5.0	3.648011	1839	1839
6.0	4.070343	1209	1209
7.0	4.425798	795	795
8.0	4.724965	561	561
9.0	4.97676	430	430
10.0	5.188682	324	324
11.0	5.367046	248	248
12.0	5.517165	197	197
13.0	5.643513	181	181
14.0	5.749854	154	154
15.0	5.839355	113	113
16.0	5.914684	141	141
17.0	5.978084	117	117
18.0	6.031445	119	119
19.0	6.076356	104	104
20.0	6.114155	85	85
21.0	6.145969	98	98
22.0	6.172745	96	96
23.0	6.195281	100	100
24.0	6.214248	92	92
25.0	6.230212	75	75
26.0	6.243648	79	79
27.0	6.254956	77	77
28.0	6.264474	67	67
29.0	6.272484	68	68
30.0	6.279226	57	57
31.0	6.284901	65	65
32.0	6.289676	59	59
33.0	6.293696	59	59
34.0	6.297079	58	58
35.0	6.299926	48	48
36.0	6.302323	48	48
37.0	6.30434	52	52
38.0	6.306038	51	51
39.0	6.307466	49	49
40.0	6.308669	42	42
41.0	6.309681	34	34
42.0	6.310533	44	44
43.0	6.31125	44	44
44.0	6.311853	22	22
45.0	6.312361	29	29
46.0	6.312789	27	27
47.0	6.313148	20	20
48.0	6.313451	25	25
49.0	6.313706	23	23
50.0	6.31392	24	24
51.0	6.314101	24	24
52.0	6.314253	18	18
53.0	6.314381	20	20
54.0	6.314488	24	24
55.0	6.314579	22	22
56.0	6.314655	16	16
57.0	6.314719	27	27
58.0	6.314773	17	17
59.0	6.314819	12	12
60.0	6.314857	10	10
61.0	6.314889	4	4
62.0	6.314916	13	13
63.0	6.314939	16	16
64.0	6.314958	15	15
65.0	6.314975	10	10
66.0	6.314988	11	11
67.0	6.315	15	15
68.0	6.315009	12	12
69.0	6.315017	14	14
70.0	6.315024	15	15
71.0	6.31503	9	9
72.0	6.315035	11	11
73.0	6.315039	7	7
74.0	6.315042	10	10
75.0	6.315045	11	11
76.0	6.315048	12	12
77.0	6.31505	10	10
78.0	6.315051	14	14
79.0	6.315053	8	8
80.0	6.315054	12	12
81.0	6.315055	12	12
82.0	6.315056	10	10
83.0	6.315057	9	9
84.0	6.315057	7	7
85.0	6.315058	7	7
86.0	6.315058	3	3
87.0	6.315058	7	7
88.0	6.315059	5	5
89.0	6.315059	9	9
90.0	6.315059	11	11
91.0	6.315059	6	6
92.0	6.31506	8	8
93.0	6.31506	8	8
94.0	6.31506	10	10
95.0	6.31506	8	8
96.0	6.31506	4	4
97.0	6.31506	11	11
98.0	6.31506	4	4
99.0	6.31506	10	10
100.0	6.31506	11	11
101.0	0	9	9
102.0	0	9	9
103.0	0	11	11
104.0	0	2	2
105.0	0	10	10
106.0	0	5	5
107.0	0	9	9
108.0	0	8	8
109.0	0	6	6
110.0	0	7	7
111.0	0	7	7
112.0	0	8	8
113.0	0	3	3
114.0	0	8	8
115.0	0	4	4
116.0	0	5	5
117.0	0	4	4
118.0	0	7	7
119.0	0	3	3
120.0	0	9	9
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
124.0	0	8	8
125.0	0	6	6
126.0	0	2	2
127.0	0	6	6
128.0	0	8	8
129.0	0	4	4
130.0	0	5	5
131.0	0	7	7
132.0	0	8	8
133.0	0	4	4
134.0	0	5	5
135.0	0	8	8
136.0	0	3	3
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
140.0	0	7	7
141.0	0	2	2
142.0	0	7	7
143.0	0	2	2
144.0	0	3	3
145.0	0	3	3
146.0	0	3	3
147.0	0	2	2
148.0	0	3	3
149.0	0	4	4
150.0	0	5	5
151.0	0	2	2
152.0	0	3	3
153.0	0	5	5
154.0	0	2	2
155.0	0	4	4
156.0	0	5	5
157.0	0	2	2
158.0	0	5	5
159.0	0	3	3
160.0	0	2	2
161.0	0	1	1
162.0	0	1	1
163.0	0	4	4
164.0	0	2	2
165.0	0	2	2
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	7	7
173.0	0	6	6
174.0	0	1	1
175.0	0	3	3
176.0	0	3	3
177.0	0	3	3
178.0	0	2	2
179.0	0	3	3
180.0	0	1	1
182.0	0	2	2
183.0	0	1	1
184.0	0	3	3
185.0	0	3	3
186.0	0	1	1
187.0	0	1	1
188.0	0	2	2
189.0	0	2	2
190.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	2	2
198.0	0	1	1
199.0	0	2	2
200.0	0	1	1
202.0	0	2	2
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
211.0	0	4	4
212.0	0	2	2
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
224.0	0	2	2
225.0	0	2	2
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
231.0	0	2	2
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	2	2
240.0	0	1	1
245.0	0	1	1
248.0	0	1	1
251.0	0	1	1
252.0	0	1	1
254.0	0	1	1
258.0	0	1	1
260.0	0	1	1
265.0	0	1	1
269.0	0	2	2
273.0	0	2	2
275.0	0	1	1
276.0	0	1	1
298.0	0	1	1
301.0	0	1	1
305.0	0	1	1
306.0	0	1	1
307.0	0	1	1
310.0	0	1	1
311.0	0	1	1
313.0	0	1	1
323.0	0	2	2
325.0	0	1	1
327.0	0	1	1
328.0	0	1	1
335.0	0	1	1
336.0	0	1	1
338.0	0	2	2
341.0	0	1	1
349.0	0	1	1
354.0	0	1	1
362.0	0	1	1
365.0	0	1	1
369.0	0	1	1
377.0	0	2	2
378.0	0	1	1
383.0	0	1	1
384.0	0	2	2
390.0	0	1	1
391.0	0	1	1
396.0	0	2	2
398.0	0	1	1
402.0	0	1	1
405.0	0	1	1
408.0	0	2	2
413.0	0	1	1
420.0	0	1	1
422.0	0	1	1
431.0	0	1	1
432.0	0	1	1
436.0	0	1	1
452.0	0	1	1
453.0	0	1	1
458.0	0	1	1
484.0	0	1	1
489.0	0	2	2
492.0	0	1	1
494.0	0	1	1
495.0	0	1	1
503.0	0	1	1
505.0	0	1	1
520.0	0	1	1
532.0	0	1	1
562.0	0	1	1
567.0	0	1	1
602.0	0	1	1
656.0	0	1	1
658.0	0	1	1
814.0	0	2	2
909.0	0	1	1
948.0	0	1	1
1066.0	0	1	1
1101.0	0	1	1
1114.0	0	1	1
1496.0	0	1	1
2629.0	0	1	1