## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-06-08/DK_Mid_Kar_1_2016-06-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-06-08/DK_Mid_Kar_1_2016-06-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2016-06-08/DK_Mid_Kar_1_2016-06-08.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 09:14:56 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	37522914	13249465	0	0	9588698	1092659	0	0.183906	75850772

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11053748	11053748
2.0	1.839727	734303	734303
3.0	2.544869	57179	57179
4.0	3.136996	6996	6996
5.0	3.634222	2311	2311
6.0	4.051755	1382	1382
7.0	4.402369	939	939
8.0	4.69679	722	722
9.0	4.944023	595	595
10.0	5.151631	377	377
11.0	5.325965	323	323
12.0	5.472359	298	298
13.0	5.595289	212	212
14.0	5.698517	199	199
15.0	5.785201	182	182
16.0	5.857991	164	164
17.0	5.919115	157	157
18.0	5.970443	124	124
19.0	6.013544	121	121
20.0	6.049737	108	108
21.0	6.08013	107	107
22.0	6.105651	109	109
23.0	6.127082	92	92
24.0	6.145078	89	89
25.0	6.16019	97	97
26.0	6.17288	85	85
27.0	6.183536	107	107
28.0	6.192484	71	71
29.0	6.199998	74	74
30.0	6.206308	63	63
31.0	6.211606	61	61
32.0	6.216056	50	50
33.0	6.219792	45	45
34.0	6.222929	59	59
35.0	6.225564	57	57
36.0	6.227776	41	41
37.0	6.229634	46	46
38.0	6.231194	33	33
39.0	6.232504	26	26
40.0	6.233604	26	26
41.0	6.234527	21	21
42.0	6.235303	32	32
43.0	6.235954	23	23
44.0	6.236501	25	25
45.0	6.23696	29	29
46.0	6.237346	22	22
47.0	6.23767	22	22
48.0	6.237942	19	19
49.0	6.23817	23	23
50.0	6.238362	20	20
51.0	6.238523	23	23
52.0	6.238658	19	19
53.0	6.238772	13	13
54.0	6.238867	18	18
55.0	6.238947	19	19
56.0	6.239015	11	11
57.0	6.239071	16	16
58.0	6.239118	12	12
59.0	6.239158	14	14
60.0	6.239192	13	13
61.0	6.23922	9	9
62.0	6.239243	17	17
63.0	6.239263	20	20
64.0	6.23928	17	17
65.0	6.239294	11	11
66.0	6.239305	16	16
67.0	6.239315	10	10
68.0	6.239324	12	12
69.0	6.23933	11	11
70.0	6.239336	8	8
71.0	6.239341	12	12
72.0	6.239345	13	13
73.0	6.239349	12	12
74.0	6.239352	13	13
75.0	6.239354	3	3
76.0	6.239356	15	15
77.0	6.239358	10	10
78.0	6.239359	15	15
79.0	6.23936	13	13
80.0	6.239361	10	10
81.0	6.239362	11	11
82.0	6.239363	8	8
83.0	6.239364	6	6
84.0	6.239364	13	13
85.0	6.239365	9	9
86.0	6.239365	9	9
87.0	6.239365	11	11
88.0	6.239366	11	11
89.0	6.239366	7	7
90.0	6.239366	7	7
91.0	6.239366	11	11
92.0	6.239366	5	5
93.0	6.239366	5	5
94.0	6.239366	7	7
95.0	6.239366	7	7
96.0	6.239366	11	11
97.0	6.239367	6	6
98.0	6.239367	10	10
99.0	6.239367	6	6
100.0	6.239367	11	11
101.0	0	4	4
102.0	0	9	9
103.0	0	7	7
104.0	0	4	4
105.0	0	4	4
106.0	0	3	3
107.0	0	6	6
108.0	0	9	9
109.0	0	2	2
110.0	0	7	7
111.0	0	5	5
112.0	0	4	4
113.0	0	4	4
114.0	0	3	3
116.0	0	4	4
117.0	0	3	3
118.0	0	4	4
119.0	0	5	5
120.0	0	7	7
121.0	0	1	1
122.0	0	3	3
123.0	0	2	2
124.0	0	1	1
125.0	0	4	4
126.0	0	5	5
127.0	0	4	4
128.0	0	1	1
129.0	0	4	4
130.0	0	6	6
131.0	0	1	1
132.0	0	3	3
133.0	0	2	2
134.0	0	5	5
136.0	0	2	2
137.0	0	4	4
138.0	0	3	3
139.0	0	3	3
140.0	0	3	3
141.0	0	2	2
142.0	0	2	2
143.0	0	2	2
144.0	0	1	1
145.0	0	3	3
146.0	0	3	3
147.0	0	1	1
148.0	0	2	2
149.0	0	5	5
150.0	0	1	1
151.0	0	1	1
153.0	0	5	5
154.0	0	2	2
155.0	0	3	3
157.0	0	3	3
158.0	0	1	1
159.0	0	3	3
161.0	0	4	4
162.0	0	1	1
163.0	0	1	1
164.0	0	2	2
165.0	0	1	1
166.0	0	3	3
167.0	0	2	2
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
178.0	0	1	1
181.0	0	3	3
182.0	0	1	1
184.0	0	2	2
186.0	0	2	2
189.0	0	1	1
190.0	0	2	2
191.0	0	2	2
193.0	0	2	2
194.0	0	3	3
195.0	0	1	1
197.0	0	2	2
198.0	0	1	1
200.0	0	1	1
201.0	0	1	1
203.0	0	1	1
205.0	0	1	1
207.0	0	1	1
209.0	0	1	1
211.0	0	1	1
212.0	0	2	2
213.0	0	2	2
214.0	0	1	1
215.0	0	2	2
216.0	0	2	2
223.0	0	1	1
225.0	0	2	2
228.0	0	1	1
230.0	0	1	1
238.0	0	2	2
240.0	0	2	2
242.0	0	1	1
245.0	0	1	1
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	2	2
252.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
266.0	0	1	1
272.0	0	1	1
275.0	0	1	1
278.0	0	1	1
282.0	0	1	1
286.0	0	1	1
287.0	0	2	2
288.0	0	2	2
290.0	0	1	1
292.0	0	1	1
295.0	0	1	1
299.0	0	1	1
302.0	0	1	1
305.0	0	1	1
309.0	0	1	1
314.0	0	1	1
316.0	0	2	2
319.0	0	1	1
325.0	0	1	1
327.0	0	2	2
329.0	0	1	1
332.0	0	1	1
334.0	0	1	1
335.0	0	1	1
351.0	0	1	1
352.0	0	1	1
356.0	0	1	1
357.0	0	1	1
361.0	0	1	1
362.0	0	1	1
371.0	0	1	1
383.0	0	2	2
385.0	0	1	1
388.0	0	1	1
391.0	0	1	1
397.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	2	2
412.0	0	1	1
416.0	0	1	1
437.0	0	1	1
444.0	0	1	1
529.0	0	1	1
558.0	0	1	1
579.0	0	1	1
669.0	0	1	1
695.0	0	1	1
703.0	0	1	1
717.0	0	1	1
881.0	0	1	1
939.0	0	1	1
1064.0	0	1	1
1075.0	0	1	1
1313.0	0	1	1
1314.0	0	1	1
1353.0	0	1	1
1597.0	0	1	1
3027.0	0	1	1