## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-10-11/UA_Kie_Kyi_1_2014-10-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-10-11/UA_Kie_Kyi_1_2014-10-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-10-11/UA_Kie_Kyi_1_2014-10-11.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 16:50:40 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	2702244	18920136	0	0	514782	558667	0	0.040257	314041823

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17578111	17578111
2.0	1.941532	393900	393900
3.0	2.828014	7949	7949
4.0	3.662665	683	683
5.0	4.448515	363	363
6.0	5.188419	263	263
7.0	5.885061	209	209
8.0	6.540972	170	170
9.0	7.158533	150	150
10.0	7.739986	118	118
11.0	8.287443	99	99
12.0	8.802891	108	108
13.0	9.288201	97	97
14.0	9.745137	84	84
15.0	10.175356	77	77
16.0	10.580421	80	80
17.0	10.961802	64	64
18.0	11.320885	56	56
19.0	11.658973	59	59
20.0	11.977294	53	53
21.0	12.277002	41	41
22.0	12.559188	46	46
23.0	12.824874	38	38
24.0	13.075027	22	22
25.0	13.310553	30	30
26.0	13.532309	38	38
27.0	13.741098	32	32
28.0	13.937681	30	30
29.0	14.122769	27	27
30.0	14.297036	24	24
31.0	14.461114	26	26
32.0	14.615598	38	38
33.0	14.76105	27	27
34.0	14.897997	24	24
35.0	15.026938	22	22
36.0	15.148339	30	30
37.0	15.262643	24	24
38.0	15.370263	22	22
39.0	15.471591	16	16
40.0	15.566995	18	18
41.0	15.65682	14	14
42.0	15.741393	22	22
43.0	15.821022	14	14
44.0	15.895995	18	18
45.0	15.966584	21	21
46.0	16.033046	13	13
47.0	16.095623	16	16
48.0	16.15454	13	13
49.0	16.210013	17	17
50.0	16.262242	17	17
51.0	16.311418	9	9
52.0	16.357718	10	10
53.0	16.401311	11	11
54.0	16.442355	7	7
55.0	16.481	4	4
56.0	16.517385	5	5
57.0	16.551643	16	16
58.0	16.583898	13	13
59.0	16.614267	10	10
60.0	16.64286	10	10
61.0	16.669781	4	4
62.0	16.695129	12	12
63.0	16.718994	9	9
64.0	16.741464	8	8
65.0	16.76262	8	8
66.0	16.78254	9	9
67.0	16.801294	8	8
68.0	16.818952	11	11
69.0	16.835578	7	7
70.0	16.851232	6	6
71.0	16.86597	3	3
72.0	16.879847	7	7
73.0	16.892912	5	5
74.0	16.905213	6	6
75.0	16.916795	7	7
76.0	16.9277	4	4
77.0	16.937968	6	6
78.0	16.947635	9	9
79.0	16.956737	4	4
80.0	16.965306	5	5
81.0	16.973375	10	10
82.0	16.980972	8	8
83.0	16.988124	2	2
84.0	16.994859	8	8
85.0	17.0012	7	7
86.0	17.00717	5	5
87.0	17.01279	6	6
88.0	17.018083	8	8
89.0	17.023066	5	5
90.0	17.027757	2	2
91.0	17.032174	5	5
92.0	17.036333	5	5
93.0	17.040249	5	5
94.0	17.043936	0	0
95.0	17.047407	5	5
96.0	17.050675	4	4
97.0	17.053753	8	8
98.0	17.05665	3	3
99.0	17.059378	3	3
100.0	17.061946	3	3
101.0	0	7	7
102.0	0	1	1
104.0	0	4	4
105.0	0	2	2
106.0	0	4	4
107.0	0	2	2
108.0	0	4	4
109.0	0	4	4
110.0	0	3	3
111.0	0	4	4
112.0	0	7	7
113.0	0	7	7
114.0	0	2	2
115.0	0	5	5
116.0	0	7	7
117.0	0	3	3
118.0	0	4	4
119.0	0	7	7
120.0	0	3	3
121.0	0	7	7
122.0	0	1	1
123.0	0	4	4
124.0	0	2	2
125.0	0	1	1
126.0	0	6	6
128.0	0	2	2
129.0	0	2	2
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
133.0	0	3	3
134.0	0	5	5
135.0	0	4	4
137.0	0	5	5
138.0	0	2	2
139.0	0	4	4
140.0	0	3	3
141.0	0	3	3
142.0	0	3	3
144.0	0	2	2
145.0	0	7	7
146.0	0	1	1
147.0	0	5	5
148.0	0	1	1
149.0	0	2	2
151.0	0	7	7
152.0	0	2	2
153.0	0	3	3
154.0	0	2	2
155.0	0	3	3
158.0	0	2	2
160.0	0	3	3
162.0	0	2	2
163.0	0	2	2
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
169.0	0	2	2
170.0	0	2	2
171.0	0	5	5
173.0	0	2	2
174.0	0	1	1
175.0	0	5	5
176.0	0	3	3
177.0	0	1	1
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
186.0	0	1	1
187.0	0	4	4
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
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
203.0	0	1	1
204.0	0	4	4
206.0	0	1	1
207.0	0	3	3
208.0	0	1	1
210.0	0	1	1
212.0	0	2	2
213.0	0	1	1
215.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
222.0	0	1	1
223.0	0	4	4
226.0	0	2	2
227.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	2	2
233.0	0	1	1
237.0	0	1	1
239.0	0	1	1
241.0	0	2	2
243.0	0	1	1
244.0	0	1	1
245.0	0	2	2
246.0	0	1	1
247.0	0	1	1
250.0	0	2	2
252.0	0	1	1
253.0	0	2	2
256.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	3	3
260.0	0	2	2
261.0	0	1	1
265.0	0	1	1
267.0	0	2	2
269.0	0	1	1
271.0	0	1	1
272.0	0	1	1
278.0	0	2	2
279.0	0	2	2
281.0	0	1	1
285.0	0	2	2
287.0	0	1	1
288.0	0	1	1
290.0	0	2	2
291.0	0	2	2
298.0	0	1	1
301.0	0	1	1
302.0	0	1	1
305.0	0	2	2
306.0	0	2	2
311.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	2	2
328.0	0	2	2
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
338.0	0	1	1
339.0	0	1	1
341.0	0	2	2
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	1	1
361.0	0	1	1
373.0	0	2	2
382.0	0	1	1
383.0	0	1	1
385.0	0	1	1
399.0	0	1	1
407.0	0	1	1
410.0	0	1	1
414.0	0	1	1
415.0	0	1	1
417.0	0	1	1
424.0	0	1	1
425.0	0	1	1
430.0	0	2	2
440.0	0	1	1
443.0	0	1	1
455.0	0	1	1
471.0	0	1	1
483.0	0	2	2
485.0	0	1	1
497.0	0	1	1
504.0	0	1	1
510.0	0	1	1
516.0	0	1	1
518.0	0	1	1
522.0	0	1	1
532.0	0	1	1
533.0	0	1	1
539.0	0	1	1
544.0	0	1	1
549.0	0	1	1
566.0	0	1	1
571.0	0	1	1
589.0	0	1	1
595.0	0	1	1
607.0	0	1	1
661.0	0	1	1
701.0	0	1	1
785.0	0	1	1
824.0	0	1	1