## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-10-23/DE_Bad_Bro_1_2016-10-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-10-23/DE_Bad_Bro_1_2016-10-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2016-10-23/DE_Bad_Bro_1_2016-10-23.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 08:58:46 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	28680017	12688547	0	0	6788130	1014668	0	0.163114	75047486

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10598196	10598196
2.0	1.844447	713049	713049
3.0	2.557537	54521	54521
4.0	3.159704	6204	6204
5.0	3.668202	1887	1887
6.0	4.097601	1156	1156
7.0	4.460206	788	788
8.0	4.766407	610	610
9.0	5.024977	425	425
10.0	5.243325	335	335
11.0	5.427709	282	282
12.0	5.583411	289	289
13.0	5.714894	229	229
14.0	5.825924	178	178
15.0	5.919682	153	153
16.0	5.998857	154	154
17.0	6.065715	148	148
18.0	6.122173	126	126
19.0	6.16985	141	141
20.0	6.21011	122	122
21.0	6.244107	109	109
22.0	6.272816	105	105
23.0	6.297059	99	99
24.0	6.317531	86	86
25.0	6.334819	76	76
26.0	6.349417	72	72
27.0	6.361745	62	62
28.0	6.372155	60	60
29.0	6.380946	58	58
30.0	6.388369	64	64
31.0	6.394637	49	49
32.0	6.399931	35	35
33.0	6.404401	34	34
34.0	6.408176	42	42
35.0	6.411363	41	41
36.0	6.414055	29	29
37.0	6.416328	30	30
38.0	6.418247	25	25
39.0	6.419868	26	26
40.0	6.421237	29	29
41.0	6.422393	22	22
42.0	6.423369	22	22
43.0	6.424193	20	20
44.0	6.424889	22	22
45.0	6.425477	28	28
46.0	6.425973	19	19
47.0	6.426392	23	23
48.0	6.426746	19	19
49.0	6.427045	21	21
50.0	6.427297	10	10
51.0	6.427511	13	13
52.0	6.42769	24	24
53.0	6.427842	17	17
54.0	6.427971	6	6
55.0	6.428079	22	22
56.0	6.428171	19	19
57.0	6.428248	17	17
58.0	6.428313	13	13
59.0	6.428368	11	11
60.0	6.428415	14	14
61.0	6.428454	15	15
62.0	6.428487	11	11
63.0	6.428515	9	9
64.0	6.428539	16	16
65.0	6.428559	14	14
66.0	6.428576	11	11
67.0	6.42859	19	19
68.0	6.428602	10	10
69.0	6.428612	17	17
70.0	6.428621	18	18
71.0	6.428628	12	12
72.0	6.428634	16	16
73.0	6.428639	9	9
74.0	6.428644	7	7
75.0	6.428647	13	13
76.0	6.428651	10	10
77.0	6.428653	8	8
78.0	6.428655	14	14
79.0	6.428657	14	14
80.0	6.428659	7	7
81.0	6.42866	8	8
82.0	6.428661	10	10
83.0	6.428662	8	8
84.0	6.428663	14	14
85.0	6.428664	8	8
86.0	6.428664	7	7
87.0	6.428665	5	5
88.0	6.428665	8	8
89.0	6.428666	7	7
90.0	6.428666	8	8
91.0	6.428666	6	6
92.0	6.428666	4	4
93.0	6.428667	5	5
94.0	6.428667	5	5
95.0	6.428667	8	8
96.0	6.428667	3	3
97.0	6.428667	5	5
98.0	6.428667	3	3
99.0	6.428667	8	8
100.0	6.428667	6	6
101.0	0	3	3
102.0	0	5	5
103.0	0	5	5
104.0	0	7	7
105.0	0	5	5
106.0	0	5	5
107.0	0	7	7
109.0	0	2	2
110.0	0	5	5
111.0	0	5	5
112.0	0	5	5
113.0	0	1	1
114.0	0	2	2
117.0	0	1	1
118.0	0	1	1
119.0	0	5	5
120.0	0	4	4
122.0	0	3	3
123.0	0	6	6
125.0	0	3	3
127.0	0	5	5
128.0	0	7	7
129.0	0	1	1
130.0	0	1	1
133.0	0	3	3
136.0	0	2	2
137.0	0	1	1
138.0	0	4	4
139.0	0	1	1
140.0	0	2	2
141.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	2	2
145.0	0	1	1
146.0	0	1	1
147.0	0	4	4
148.0	0	3	3
149.0	0	4	4
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	2	2
157.0	0	5	5
158.0	0	1	1
159.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	2	2
166.0	0	4	4
167.0	0	2	2
170.0	0	2	2
172.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
182.0	0	1	1
184.0	0	1	1
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
201.0	0	1	1
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
208.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
221.0	0	1	1
222.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
231.0	0	1	1
233.0	0	1	1
238.0	0	1	1
239.0	0	1	1
242.0	0	1	1
245.0	0	1	1
247.0	0	2	2
248.0	0	1	1
249.0	0	1	1
251.0	0	2	2
254.0	0	1	1
256.0	0	2	2
257.0	0	1	1
259.0	0	1	1
261.0	0	1	1
267.0	0	3	3
270.0	0	1	1
271.0	0	1	1
279.0	0	1	1
282.0	0	1	1
286.0	0	1	1
304.0	0	1	1
309.0	0	1	1
311.0	0	1	1
314.0	0	1	1
320.0	0	1	1
323.0	0	1	1
333.0	0	1	1
340.0	0	1	1
341.0	0	1	1
344.0	0	1	1
363.0	0	1	1
373.0	0	1	1
380.0	0	1	1
403.0	0	1	1
424.0	0	1	1
475.0	0	1	1
550.0	0	1	1
567.0	0	1	1
632.0	0	1	1
673.0	0	1	1
711.0	0	1	1
780.0	0	1	1
1504.0	0	1	1