## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-09-04/UA_Kie_Kyi_1_2016-09-04.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-09-04/UA_Kie_Kyi_1_2016-09-04.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2016-09-04/UA_Kie_Kyi_1_2016-09-04.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 17:36:34 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	30401662	10835733	0	0	8008806	900169	0	0.188372	61552992

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9011043	9011043
2.0	1.838585	569690	569690
3.0	2.54181	42905	42905
4.0	3.131525	5376	5376
5.0	3.62605	1880	1880
6.0	4.040752	1188	1188
7.0	4.388515	764	764
8.0	4.680144	629	629
9.0	4.924699	436	436
10.0	5.12978	366	366
11.0	5.301757	284	284
12.0	5.445975	250	250
13.0	5.566914	194	194
14.0	5.668332	178	178
15.0	5.753379	183	183
16.0	5.824699	161	161
17.0	5.884506	141	141
18.0	5.93466	131	131
19.0	5.976718	121	121
20.0	6.011987	98	98
21.0	6.041563	122	122
22.0	6.066366	123	123
23.0	6.087164	100	100
24.0	6.104606	99	99
25.0	6.119232	67	67
26.0	6.131498	67	67
27.0	6.141783	64	64
28.0	6.150408	80	80
29.0	6.157641	58	58
30.0	6.163707	55	55
31.0	6.168793	69	69
32.0	6.173059	56	56
33.0	6.176636	58	58
34.0	6.179635	41	41
35.0	6.182151	38	38
36.0	6.18426	31	31
37.0	6.186029	48	48
38.0	6.187512	51	51
39.0	6.188756	33	33
40.0	6.189799	34	34
41.0	6.190674	43	43
42.0	6.191408	24	24
43.0	6.192023	25	25
44.0	6.192539	32	32
45.0	6.192971	13	13
46.0	6.193334	27	27
47.0	6.193638	20	20
48.0	6.193893	33	33
49.0	6.194107	21	21
50.0	6.194287	26	26
51.0	6.194437	18	18
52.0	6.194563	21	21
53.0	6.194669	20	20
54.0	6.194758	16	16
55.0	6.194832	28	28
56.0	6.194895	18	18
57.0	6.194947	14	14
58.0	6.194991	22	22
59.0	6.195028	13	13
60.0	6.195058	13	13
61.0	6.195084	14	14
62.0	6.195106	13	13
63.0	6.195124	7	7
64.0	6.195139	8	8
65.0	6.195152	14	14
66.0	6.195163	13	13
67.0	6.195172	17	17
68.0	6.19518	6	6
69.0	6.195186	10	10
70.0	6.195191	9	9
71.0	6.195196	19	19
72.0	6.195199	15	15
73.0	6.195202	17	17
74.0	6.195205	12	12
75.0	6.195207	9	9
76.0	6.195209	14	14
77.0	6.195211	11	11
78.0	6.195212	7	7
79.0	6.195213	12	12
80.0	6.195214	16	16
81.0	6.195215	8	8
82.0	6.195215	11	11
83.0	6.195216	11	11
84.0	6.195216	6	6
85.0	6.195217	10	10
86.0	6.195217	10	10
87.0	6.195217	13	13
88.0	6.195218	8	8
89.0	6.195218	6	6
90.0	6.195218	12	12
91.0	6.195218	6	6
92.0	6.195218	9	9
93.0	6.195218	6	6
94.0	6.195218	10	10
95.0	6.195218	13	13
96.0	6.195218	4	4
97.0	6.195218	9	9
98.0	6.195219	5	5
99.0	6.195219	6	6
100.0	6.195219	8	8
101.0	0	7	7
102.0	0	8	8
103.0	0	3	3
104.0	0	7	7
105.0	0	8	8
106.0	0	9	9
107.0	0	5	5
108.0	0	8	8
109.0	0	4	4
110.0	0	8	8
111.0	0	5	5
112.0	0	2	2
113.0	0	7	7
114.0	0	6	6
115.0	0	1	1
116.0	0	1	1
117.0	0	6	6
118.0	0	5	5
119.0	0	5	5
120.0	0	6	6
121.0	0	3	3
122.0	0	3	3
123.0	0	7	7
124.0	0	2	2
125.0	0	5	5
126.0	0	4	4
127.0	0	6	6
128.0	0	1	1
130.0	0	2	2
131.0	0	3	3
132.0	0	5	5
133.0	0	3	3
134.0	0	4	4
135.0	0	4	4
136.0	0	4	4
137.0	0	1	1
138.0	0	4	4
139.0	0	7	7
140.0	0	2	2
141.0	0	2	2
142.0	0	4	4
143.0	0	3	3
144.0	0	7	7
145.0	0	4	4
146.0	0	3	3
148.0	0	1	1
149.0	0	3	3
150.0	0	5	5
151.0	0	4	4
152.0	0	1	1
154.0	0	2	2
155.0	0	3	3
157.0	0	2	2
158.0	0	1	1
159.0	0	10	10
160.0	0	4	4
161.0	0	1	1
162.0	0	2	2
164.0	0	2	2
166.0	0	1	1
167.0	0	3	3
168.0	0	2	2
169.0	0	3	3
171.0	0	3	3
172.0	0	2	2
173.0	0	2	2
174.0	0	2	2
176.0	0	3	3
177.0	0	3	3
181.0	0	2	2
185.0	0	2	2
187.0	0	1	1
188.0	0	1	1
190.0	0	2	2
195.0	0	2	2
197.0	0	2	2
198.0	0	1	1
200.0	0	3	3
202.0	0	2	2
204.0	0	1	1
207.0	0	2	2
208.0	0	2	2
211.0	0	1	1
213.0	0	1	1
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
223.0	0	1	1
224.0	0	1	1
226.0	0	1	1
227.0	0	1	1
231.0	0	2	2
232.0	0	2	2
233.0	0	2	2
234.0	0	2	2
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	1	1
243.0	0	1	1
244.0	0	1	1
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
260.0	0	1	1
263.0	0	2	2
266.0	0	1	1
267.0	0	1	1
270.0	0	1	1
272.0	0	1	1
273.0	0	1	1
274.0	0	1	1
277.0	0	1	1
278.0	0	1	1
281.0	0	1	1
283.0	0	1	1
288.0	0	1	1
290.0	0	1	1
291.0	0	1	1
292.0	0	1	1
295.0	0	2	2
296.0	0	1	1
297.0	0	1	1
300.0	0	1	1
303.0	0	1	1
304.0	0	1	1
306.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
313.0	0	2	2
314.0	0	1	1
316.0	0	1	1
317.0	0	1	1
325.0	0	2	2
327.0	0	1	1
332.0	0	1	1
340.0	0	1	1
346.0	0	2	2
348.0	0	2	2
350.0	0	2	2
352.0	0	1	1
354.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	1	1
373.0	0	1	1
396.0	0	1	1
399.0	0	1	1
407.0	0	1	1
410.0	0	1	1
422.0	0	1	1
433.0	0	1	1
437.0	0	1	1
447.0	0	1	1
466.0	0	1	1
469.0	0	1	1
471.0	0	1	1
479.0	0	1	1
486.0	0	1	1
498.0	0	1	1
501.0	0	1	1
502.0	0	1	1
523.0	0	1	1
531.0	0	1	1
571.0	0	1	1
606.0	0	1	1
626.0	0	1	1
705.0	0	2	2
711.0	0	1	1
718.0	0	1	1
759.0	0	1	1
783.0	0	1	1
910.0	0	1	1
970.0	0	1	1
1006.0	0	1	1
1161.0	0	1	1
1876.0	0	1	1
3962.0	0	1	1