## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Ben_1_2016-10-08/ES_Gra_Ben_1_2016-10-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Ben_1_2016-10-08/ES_Gra_Ben_1_2016-10-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Ben_1_2016-10-08/ES_Gra_Ben_1_2016-10-08.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 08:49:44 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	26696512	8254330	0	0	5897835	662342	0	0.167168	48644221

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	6906865	6906865
2.0	1.843928	430310	430310
3.0	2.556143	32224	32224
4.0	3.157201	3856	3856
5.0	3.664452	1236	1236
6.0	4.092534	795	795
7.0	4.453805	510	510
8.0	4.758692	338	338
9.0	5.015995	260	260
10.0	5.23314	236	236
11.0	5.416395	193	193
12.0	5.571049	162	162
13.0	5.701565	143	143
14.0	5.811712	137	137
15.0	5.904668	123	123
16.0	5.983116	111	111
17.0	6.049321	120	120
18.0	6.105193	95	95
19.0	6.152345	100	100
20.0	6.192138	89	89
21.0	6.22572	82	82
22.0	6.254061	96	96
23.0	6.277979	86	86
24.0	6.298164	71	71
25.0	6.315199	72	72
26.0	6.329575	71	71
27.0	6.341707	72	72
28.0	6.351946	53	53
29.0	6.360586	48	48
30.0	6.367879	45	45
31.0	6.374033	48	48
32.0	6.379226	40	40
33.0	6.38361	53	53
34.0	6.387308	52	52
35.0	6.39043	36	36
36.0	6.393065	29	29
37.0	6.395288	37	37
38.0	6.397164	18	18
39.0	6.398748	24	24
40.0	6.400084	23	23
41.0	6.401212	29	29
42.0	6.402164	26	26
43.0	6.402967	20	20
44.0	6.403645	18	18
45.0	6.404217	17	17
46.0	6.4047	13	13
47.0	6.405107	13	13
48.0	6.405451	18	18
49.0	6.405741	12	12
50.0	6.405986	18	18
51.0	6.406193	16	16
52.0	6.406367	28	28
53.0	6.406514	21	21
54.0	6.406638	18	18
55.0	6.406743	11	11
56.0	6.406832	13	13
57.0	6.406906	13	13
58.0	6.406969	6	6
59.0	6.407023	10	10
60.0	6.407067	8	8
61.0	6.407105	11	11
62.0	6.407137	12	12
63.0	6.407164	21	21
64.0	6.407187	15	15
65.0	6.407206	11	11
66.0	6.407222	15	15
67.0	6.407236	6	6
68.0	6.407248	12	12
69.0	6.407257	7	7
70.0	6.407266	11	11
71.0	6.407273	15	15
72.0	6.407278	15	15
73.0	6.407283	10	10
74.0	6.407287	8	8
75.0	6.407291	13	13
76.0	6.407294	7	7
77.0	6.407296	9	9
78.0	6.407299	10	10
79.0	6.4073	6	6
80.0	6.407302	13	13
81.0	6.407303	13	13
82.0	6.407304	11	11
83.0	6.407305	7	7
84.0	6.407306	10	10
85.0	6.407307	14	14
86.0	6.407307	5	5
87.0	6.407308	6	6
88.0	6.407308	6	6
89.0	6.407308	6	6
90.0	6.407309	6	6
91.0	6.407309	8	8
92.0	6.407309	7	7
93.0	6.407309	9	9
94.0	6.407309	9	9
95.0	6.407309	11	11
96.0	6.40731	4	4
97.0	6.40731	4	4
98.0	6.40731	2	2
99.0	6.40731	5	5
100.0	6.40731	5	5
101.0	0	3	3
102.0	0	6	6
103.0	0	9	9
104.0	0	1	1
105.0	0	5	5
106.0	0	2	2
107.0	0	5	5
108.0	0	5	5
109.0	0	2	2
110.0	0	7	7
111.0	0	3	3
112.0	0	3	3
113.0	0	1	1
114.0	0	3	3
115.0	0	2	2
116.0	0	1	1
117.0	0	5	5
118.0	0	1	1
119.0	0	2	2
120.0	0	4	4
121.0	0	3	3
122.0	0	4	4
123.0	0	3	3
124.0	0	2	2
125.0	0	1	1
126.0	0	3	3
127.0	0	1	1
128.0	0	3	3
129.0	0	3	3
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	1	1
137.0	0	2	2
138.0	0	4	4
140.0	0	3	3
142.0	0	2	2
144.0	0	1	1
145.0	0	3	3
146.0	0	2	2
147.0	0	2	2
149.0	0	1	1
150.0	0	3	3
152.0	0	1	1
154.0	0	1	1
156.0	0	2	2
158.0	0	1	1
160.0	0	2	2
161.0	0	2	2
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	1	1
181.0	0	1	1
182.0	0	1	1
184.0	0	2	2
186.0	0	1	1
188.0	0	1	1
189.0	0	1	1
194.0	0	1	1
195.0	0	1	1
199.0	0	1	1
202.0	0	1	1
204.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
211.0	0	2	2
212.0	0	2	2
218.0	0	1	1
225.0	0	1	1
229.0	0	2	2
231.0	0	1	1
234.0	0	1	1
235.0	0	2	2
236.0	0	2	2
242.0	0	2	2
243.0	0	1	1
244.0	0	1	1
249.0	0	1	1
251.0	0	2	2
254.0	0	1	1
256.0	0	1	1
261.0	0	1	1
263.0	0	1	1
264.0	0	1	1
266.0	0	1	1
273.0	0	1	1
279.0	0	2	2
283.0	0	1	1
290.0	0	1	1
292.0	0	1	1
294.0	0	1	1
301.0	0	1	1
303.0	0	1	1
304.0	0	1	1
309.0	0	1	1
315.0	0	1	1
318.0	0	1	1
327.0	0	1	1
333.0	0	2	2
336.0	0	2	2
340.0	0	1	1
342.0	0	1	1
345.0	0	1	1
348.0	0	1	1
353.0	0	1	1
363.0	0	1	1
368.0	0	2	2
373.0	0	1	1
382.0	0	2	2
387.0	0	1	1
395.0	0	1	1
397.0	0	1	1
407.0	0	1	1
408.0	0	1	1
410.0	0	1	1
412.0	0	1	1
421.0	0	1	1
450.0	0	1	1
470.0	0	1	1
498.0	0	1	1
558.0	0	1	1
968.0	0	1	1
2092.0	0	1	1