## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PL_Pom_Gda_1_2016-08-01/PL_Pom_Gda_1_2016-08-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_Pom_Gda_1_2016-08-01/PL_Pom_Gda_1_2016-08-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_Pom_Gda_1_2016-08-01/PL_Pom_Gda_1_2016-08-01.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 09:03:59 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	28892841	14541167	0	0	7198450	1143829	0	0.163624	87515407

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	12155778	12155778
2.0	1.846915	818091	818091
3.0	2.564179	60248	60248
4.0	3.17164	6809	6809
5.0	3.686108	2067	2067
6.0	4.121819	1219	1219
7.0	4.490828	866	866
8.0	4.803347	617	617
9.0	5.068025	509	509
10.0	5.292184	394	394
11.0	5.482027	344	344
12.0	5.642808	247	247
13.0	5.778976	231	231
14.0	5.894299	200	200
15.0	5.991967	172	172
16.0	6.074684	187	187
17.0	6.144738	139	139
18.0	6.204068	150	150
19.0	6.254315	106	106
20.0	6.29687	111	111
21.0	6.332911	103	103
22.0	6.363434	101	101
23.0	6.389285	94	94
24.0	6.411178	89	89
25.0	6.42972	80	80
26.0	6.445423	60	60
27.0	6.458722	69	69
28.0	6.469986	63	63
29.0	6.479525	69	69
30.0	6.487604	73	73
31.0	6.494446	48	48
32.0	6.50024	45	45
33.0	6.505148	45	45
34.0	6.509304	43	43
35.0	6.512824	28	28
36.0	6.515806	39	39
37.0	6.51833	36	36
38.0	6.520469	24	24
39.0	6.52228	27	27
40.0	6.523813	37	37
41.0	6.525112	30	30
42.0	6.526212	30	30
43.0	6.527144	20	20
44.0	6.527933	29	29
45.0	6.528601	23	23
46.0	6.529167	22	22
47.0	6.529646	24	24
48.0	6.530052	18	18
49.0	6.530396	21	21
50.0	6.530687	12	12
51.0	6.530934	22	22
52.0	6.531143	18	18
53.0	6.53132	14	14
54.0	6.531469	27	27
55.0	6.531596	20	20
56.0	6.531704	14	14
57.0	6.531795	19	19
58.0	6.531872	15	15
59.0	6.531937	16	16
60.0	6.531992	17	17
61.0	6.532039	19	19
62.0	6.532079	24	24
63.0	6.532112	19	19
64.0	6.532141	11	11
65.0	6.532165	16	16
66.0	6.532185	16	16
67.0	6.532203	26	26
68.0	6.532217	12	12
69.0	6.53223	8	8
70.0	6.53224	10	10
71.0	6.532249	20	20
72.0	6.532257	15	15
73.0	6.532263	14	14
74.0	6.532268	11	11
75.0	6.532273	5	5
76.0	6.532277	8	8
77.0	6.53228	13	13
78.0	6.532283	13	13
79.0	6.532285	7	7
80.0	6.532287	10	10
81.0	6.532289	11	11
82.0	6.53229	10	10
83.0	6.532292	9	9
84.0	6.532293	11	11
85.0	6.532293	4	4
86.0	6.532294	4	4
87.0	6.532295	7	7
88.0	6.532295	5	5
89.0	6.532296	4	4
90.0	6.532296	5	5
91.0	6.532296	14	14
92.0	6.532297	5	5
93.0	6.532297	3	3
94.0	6.532297	8	8
95.0	6.532297	6	6
96.0	6.532297	2	2
97.0	6.532298	8	8
98.0	6.532298	6	6
99.0	6.532298	7	7
100.0	6.532298	2	2
101.0	0	6	6
102.0	0	3	3
103.0	0	3	3
104.0	0	5	5
105.0	0	6	6
106.0	0	2	2
107.0	0	5	5
108.0	0	3	3
109.0	0	1	1
110.0	0	2	2
111.0	0	3	3
112.0	0	3	3
113.0	0	2	2
114.0	0	5	5
115.0	0	4	4
116.0	0	3	3
117.0	0	3	3
118.0	0	2	2
120.0	0	1	1
121.0	0	2	2
122.0	0	2	2
123.0	0	2	2
124.0	0	2	2
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	2	2
131.0	0	4	4
133.0	0	3	3
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	4	4
139.0	0	4	4
140.0	0	2	2
141.0	0	2	2
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
145.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
155.0	0	1	1
156.0	0	2	2
160.0	0	3	3
163.0	0	2	2
164.0	0	2	2
165.0	0	2	2
166.0	0	2	2
167.0	0	3	3
171.0	0	1	1
175.0	0	1	1
176.0	0	1	1
179.0	0	2	2
180.0	0	1	1
182.0	0	1	1
183.0	0	3	3
186.0	0	1	1
187.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	2	2
200.0	0	3	3
201.0	0	2	2
202.0	0	1	1
204.0	0	1	1
206.0	0	2	2
207.0	0	2	2
209.0	0	1	1
210.0	0	1	1
211.0	0	1	1
217.0	0	1	1
220.0	0	2	2
222.0	0	1	1
226.0	0	1	1
228.0	0	2	2
229.0	0	1	1
232.0	0	2	2
235.0	0	1	1
237.0	0	1	1
240.0	0	2	2
241.0	0	1	1
244.0	0	1	1
245.0	0	1	1
249.0	0	1	1
251.0	0	1	1
253.0	0	2	2
255.0	0	1	1
258.0	0	2	2
260.0	0	1	1
271.0	0	1	1
272.0	0	2	2
273.0	0	1	1
274.0	0	1	1
278.0	0	1	1
281.0	0	1	1
289.0	0	1	1
290.0	0	1	1
292.0	0	1	1
296.0	0	1	1
299.0	0	1	1
304.0	0	1	1
305.0	0	1	1
307.0	0	1	1
311.0	0	1	1
316.0	0	1	1
318.0	0	1	1
320.0	0	1	1
321.0	0	1	1
334.0	0	1	1
338.0	0	1	1
348.0	0	1	1
366.0	0	1	1
382.0	0	1	1
402.0	0	1	1
403.0	0	1	1
407.0	0	1	1
444.0	0	1	1
478.0	0	1	1
492.0	0	1	1
498.0	0	1	1
558.0	0	1	1
615.0	0	1	1
681.0	0	1	1
812.0	0	1	1
1267.0	0	1	1