## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2016-08-08/PL_War_Brz_1_2016-08-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2016-08-08/PL_War_Brz_1_2016-08-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PL_War_Brz_1_2016-08-08/PL_War_Brz_1_2016-08-08.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 09:07:16 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	32614594	14787841	0	0	8337967	1241118	0	0.173985	83096584

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	12252925	12252925
2.0	1.836976	914622	914622
3.0	2.537505	74988	74988
4.0	3.123831	8283	8283
5.0	3.614573	1914	1914
6.0	4.025311	1035	1035
7.0	4.369089	643	643
8.0	4.656824	485	485
9.0	4.897651	339	339
10.0	5.099217	310	310
11.0	5.267923	308	308
12.0	5.409126	259	259
13.0	5.52731	215	215
14.0	5.626226	194	194
15.0	5.709018	160	160
16.0	5.778312	154	154
17.0	5.836309	154	154
18.0	5.884852	128	128
19.0	5.925481	128	128
20.0	5.959486	111	111
21.0	5.987948	106	106
22.0	6.01177	87	87
23.0	6.031708	81	81
24.0	6.048396	87	87
25.0	6.062363	80	80
26.0	6.074054	56	56
27.0	6.083838	55	55
28.0	6.092028	51	51
29.0	6.098882	60	60
30.0	6.104619	51	51
31.0	6.109421	37	37
32.0	6.113439	34	34
33.0	6.116803	45	45
34.0	6.119619	34	34
35.0	6.121975	30	30
36.0	6.123947	22	22
37.0	6.125598	31	31
38.0	6.126979	16	16
39.0	6.128136	17	17
40.0	6.129104	17	17
41.0	6.129914	22	22
42.0	6.130592	29	29
43.0	6.131159	18	18
44.0	6.131634	15	15
45.0	6.132032	23	23
46.0	6.132364	24	24
47.0	6.132643	17	17
48.0	6.132876	24	24
49.0	6.133071	15	15
50.0	6.133234	13	13
51.0	6.133371	17	17
52.0	6.133485	13	13
53.0	6.133581	18	18
54.0	6.133661	20	20
55.0	6.133728	21	21
56.0	6.133785	13	13
57.0	6.133832	19	19
58.0	6.133871	21	21
59.0	6.133904	16	16
60.0	6.133931	13	13
61.0	6.133954	15	15
62.0	6.133974	15	15
63.0	6.13399	13	13
64.0	6.134003	15	15
65.0	6.134015	11	11
66.0	6.134024	5	5
67.0	6.134032	20	20
68.0	6.134039	11	11
69.0	6.134044	18	18
70.0	6.134049	19	19
71.0	6.134053	9	9
72.0	6.134056	13	13
73.0	6.134059	8	8
74.0	6.134061	4	4
75.0	6.134063	4	4
76.0	6.134065	7	7
77.0	6.134066	4	4
78.0	6.134067	3	3
79.0	6.134068	9	9
80.0	6.134069	11	11
81.0	6.134069	7	7
82.0	6.13407	9	9
83.0	6.13407	7	7
84.0	6.134071	9	9
85.0	6.134071	5	5
86.0	6.134071	6	6
87.0	6.134072	3	3
88.0	6.134072	3	3
89.0	6.134072	3	3
90.0	6.134072	5	5
91.0	6.134072	2	2
92.0	6.134072	7	7
93.0	6.134072	5	5
94.0	6.134072	2	2
95.0	6.134072	5	5
96.0	6.134072	7	7
97.0	6.134073	2	2
98.0	6.134073	2	2
99.0	6.134073	5	5
100.0	6.134073	3	3
101.0	0	4	4
102.0	0	6	6
103.0	0	2	2
104.0	0	3	3
105.0	0	4	4
106.0	0	5	5
107.0	0	2	2
108.0	0	6	6
109.0	0	2	2
110.0	0	7	7
111.0	0	2	2
112.0	0	4	4
113.0	0	1	1
114.0	0	5	5
115.0	0	1	1
116.0	0	1	1
117.0	0	1	1
118.0	0	3	3
119.0	0	4	4
120.0	0	2	2
121.0	0	1	1
122.0	0	2	2
124.0	0	3	3
125.0	0	1	1
126.0	0	4	4
127.0	0	2	2
128.0	0	4	4
129.0	0	2	2
130.0	0	3	3
131.0	0	2	2
132.0	0	3	3
134.0	0	2	2
137.0	0	1	1
138.0	0	1	1
140.0	0	3	3
142.0	0	1	1
145.0	0	1	1
146.0	0	2	2
147.0	0	1	1
150.0	0	2	2
151.0	0	1	1
152.0	0	1	1
153.0	0	4	4
155.0	0	4	4
156.0	0	1	1
158.0	0	1	1
159.0	0	2	2
161.0	0	1	1
162.0	0	1	1
163.0	0	1	1
166.0	0	2	2
167.0	0	1	1
169.0	0	1	1
171.0	0	2	2
172.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	1	1
181.0	0	1	1
183.0	0	1	1
184.0	0	3	3
190.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	2	2
196.0	0	1	1
198.0	0	1	1
200.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
210.0	0	1	1
215.0	0	2	2
217.0	0	1	1
220.0	0	2	2
224.0	0	1	1
233.0	0	1	1
240.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
255.0	0	1	1
264.0	0	1	1
265.0	0	1	1
272.0	0	1	1
274.0	0	1	1
275.0	0	1	1
279.0	0	1	1
289.0	0	1	1
296.0	0	1	1
299.0	0	1	1
329.0	0	1	1
340.0	0	1	1
375.0	0	1	1
384.0	0	1	1
441.0	0	1	1
487.0	0	1	1
504.0	0	1	1
531.0	0	2	2
633.0	0	1	1
670.0	0	1	1
772.0	0	1	1
1003.0	0	1	1