## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-05-16/UA_Ode_Ode_1_2013-05-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-05-16/UA_Ode_Ode_1_2013-05-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-05-16/UA_Ode_Ode_1_2013-05-16.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 18:56:51 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	4022042	52345294	0	0	1833247	27018286	0	0.513922	31110238

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10481226	10481226
2.0	1.185895	6572757	6572757
3.0	1.220452	3795595	3795595
4.0	1.226876	1930856	1930856
5.0	1.22807	885468	885468
6.0	1.228292	372559	372559
7.0	1.228333	145579	145579
8.0	1.228341	53875	53875
9.0	1.228342	18810	18810
10.0	1.228342	6552	6552
11.0	1.228342	2413	2413
12.0	1.228342	937	937
13.0	1.228342	532	532
14.0	1.228342	301	301
15.0	1.228342	249	249
16.0	1.228342	191	191
17.0	1.228342	149	149
18.0	1.228342	162	162
19.0	1.228342	131	131
20.0	1.228342	116	116
21.0	1.228342	100	100
22.0	1.228342	88	88
23.0	1.228342	100	100
24.0	1.228342	73	73
25.0	1.228342	64	64
26.0	1.228342	72	72
27.0	1.228342	62	62
28.0	1.228342	64	64
29.0	1.228342	63	63
30.0	1.228342	64	64
31.0	1.228342	60	60
32.0	1.228342	64	64
33.0	1.228342	33	33
34.0	1.228342	42	42
35.0	1.228342	38	38
36.0	1.228342	36	36
37.0	1.228342	25	25
38.0	1.228342	28	28
39.0	1.228342	36	36
40.0	1.228342	37	37
41.0	1.228342	23	23
42.0	1.228342	42	42
43.0	1.228342	25	25
44.0	1.228342	21	21
45.0	1.228342	22	22
46.0	1.228342	13	13
47.0	1.228342	22	22
48.0	1.228342	20	20
49.0	1.228342	17	17
50.0	1.228342	19	19
51.0	1.228342	21	21
52.0	1.228342	18	18
53.0	1.228342	12	12
54.0	1.228342	16	16
55.0	1.228342	17	17
56.0	1.228342	20	20
57.0	1.228342	10	10
58.0	1.228342	10	10
59.0	1.228342	9	9
60.0	1.228342	8	8
61.0	1.228342	14	14
62.0	1.228342	9	9
63.0	1.228342	10	10
64.0	1.228342	12	12
65.0	1.228342	4	4
66.0	1.228342	11	11
67.0	1.228342	8	8
68.0	1.228342	11	11
69.0	1.228342	12	12
70.0	1.228342	12	12
71.0	1.228342	3	3
72.0	1.228342	7	7
73.0	1.228342	7	7
74.0	1.228342	4	4
75.0	1.228342	7	7
76.0	1.228342	6	6
77.0	1.228342	9	9
78.0	1.228342	6	6
79.0	1.228342	8	8
80.0	1.228342	7	7
81.0	1.228342	5	5
82.0	1.228342	7	7
83.0	1.228342	8	8
84.0	1.228342	8	8
85.0	1.228342	4	4
86.0	1.228342	9	9
87.0	1.228342	7	7
88.0	1.228342	3	3
89.0	1.228342	7	7
90.0	1.228342	3	3
91.0	1.228342	5	5
92.0	1.228342	9	9
93.0	1.228342	3	3
94.0	1.228342	4	4
95.0	1.228342	7	7
96.0	1.228342	3	3
97.0	1.228342	2	2
98.0	1.228342	1	1
99.0	1.228342	6	6
100.0	1.228342	2	2
102.0	0	4	4
103.0	0	3	3
104.0	0	8	8
105.0	0	4	4
106.0	0	2	2
107.0	0	4	4
108.0	0	4	4
109.0	0	3	3
110.0	0	3	3
111.0	0	7	7
112.0	0	4	4
113.0	0	1	1
114.0	0	5	5
115.0	0	2	2
116.0	0	2	2
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
121.0	0	2	2
122.0	0	1	1
123.0	0	4	4
124.0	0	1	1
125.0	0	1	1
126.0	0	2	2
127.0	0	2	2
129.0	0	2	2
130.0	0	4	4
131.0	0	1	1
132.0	0	1	1
133.0	0	3	3
134.0	0	1	1
135.0	0	3	3
138.0	0	3	3
139.0	0	4	4
140.0	0	3	3
141.0	0	3	3
142.0	0	2	2
143.0	0	3	3
144.0	0	1	1
145.0	0	3	3
146.0	0	1	1
147.0	0	2	2
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	2	2
155.0	0	1	1
156.0	0	2	2
157.0	0	3	3
158.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	3	3
163.0	0	2	2
164.0	0	1	1
165.0	0	3	3
166.0	0	3	3
168.0	0	2	2
169.0	0	1	1
170.0	0	2	2
171.0	0	2	2
172.0	0	1	1
173.0	0	2	2
176.0	0	2	2
177.0	0	5	5
179.0	0	2	2
181.0	0	2	2
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	2	2
186.0	0	2	2
188.0	0	3	3
193.0	0	2	2
194.0	0	2	2
195.0	0	1	1
196.0	0	2	2
197.0	0	1	1
198.0	0	1	1
201.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
209.0	0	1	1
211.0	0	1	1
212.0	0	1	1
215.0	0	1	1
216.0	0	1	1
218.0	0	2	2
219.0	0	1	1
222.0	0	3	3
224.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	1	1
235.0	0	1	1
243.0	0	1	1
246.0	0	1	1
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
254.0	0	1	1
263.0	0	1	1
264.0	0	1	1
273.0	0	1	1
278.0	0	2	2
285.0	0	1	1
301.0	0	1	1
303.0	0	1	1
304.0	0	2	2
305.0	0	1	1
325.0	0	1	1
335.0	0	2	2
340.0	0	1	1
349.0	0	1	1
369.0	0	1	1
375.0	0	1	1
378.0	0	1	1
387.0	0	1	1
396.0	0	1	1
408.0	0	1	1
421.0	0	1	1
426.0	0	1	1
464.0	0	1	1
465.0	0	1	1
479.0	0	1	1
496.0	0	1	1
497.0	0	1	1
503.0	0	1	1
512.0	0	1	1
523.0	0	2	2
529.0	0	1	1
577.0	0	1	1
579.0	0	1	1
606.0	0	1	1
624.0	0	1	1
641.0	0	1	1
713.0	0	1	1
745.0	0	1	1
760.0	0	1	1
1014.0	0	1	1
1030.0	0	1	1
1191.0	0	1	1
1260.0	0	1	1
1277.0	0	1	1
1522.0	0	1	1
1935.0	0	1	1
2141.0	0	1	1
4516.0	0	1	1