## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Edi_Sou_1_2014-07-14/GB_Edi_Sou_1_2014-07-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Edi_Sou_1_2014-07-14/GB_Edi_Sou_1_2014-07-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Edi_Sou_1_2014-07-14/GB_Edi_Sou_1_2014-07-14.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 08:34:30 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	3880137	22202985	0	0	885263	653755	0	0.045412	369593669

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20684461	20684461
2.0	1.941695	479795	479795
3.0	2.828484	9836	9836
4.0	3.663569	735	735
5.0	4.449964	376	376
6.0	5.190508	281	281
7.0	5.887874	226	226
8.0	6.54458	201	201
9.0	7.162997	156	156
10.0	7.745357	117	117
11.0	8.293763	116	116
12.0	8.810193	103	103
13.0	9.296513	101	101
14.0	9.754478	86	86
15.0	10.185742	82	82
16.0	10.59186	72	72
17.0	10.9743	65	65
18.0	11.334441	57	57
19.0	11.673584	66	66
20.0	11.992954	48	48
21.0	12.293702	53	53
22.0	12.576915	44	44
23.0	12.843616	34	34
24.0	13.094766	28	28
25.0	13.331274	33	33
26.0	13.553991	25	25
27.0	13.763723	30	30
28.0	13.961227	30	30
29.0	14.147215	27	27
30.0	14.322358	22	22
31.0	14.487291	18	18
32.0	14.642606	18	18
33.0	14.788866	23	23
34.0	14.926599	19	19
35.0	15.0563	23	23
36.0	15.17844	31	31
37.0	15.293458	28	28
38.0	15.40177	22	22
39.0	15.503767	24	24
40.0	15.599817	22	22
41.0	15.690266	15	15
42.0	15.775442	26	26
43.0	15.855652	12	12
44.0	15.931185	22	22
45.0	16.002315	20	20
46.0	16.069297	14	14
47.0	16.132373	8	8
48.0	16.191772	21	21
49.0	16.247708	16	16
50.0	16.300382	14	14
51.0	16.349985	16	16
52.0	16.396696	15	15
53.0	16.440683	13	13
54.0	16.482106	14	14
55.0	16.521114	11	11
56.0	16.557847	8	8
57.0	16.592439	5	5
58.0	16.625013	6	6
59.0	16.655689	8	8
60.0	16.684576	8	8
61.0	16.711778	6	6
62.0	16.737395	11	11
63.0	16.761518	6	6
64.0	16.784234	9	9
65.0	16.805626	6	6
66.0	16.825771	8	8
67.0	16.844741	8	8
68.0	16.862605	6	6
69.0	16.879428	3	3
70.0	16.89527	2	2
71.0	16.910188	7	7
72.0	16.924236	9	9
73.0	16.937465	5	5
74.0	16.949923	6	6
75.0	16.961654	7	7
76.0	16.972702	10	10
77.0	16.983105	6	6
78.0	16.992902	5	5
79.0	17.002128	6	6
80.0	17.010815	7	7
81.0	17.018996	3	3
82.0	17.026701	7	7
83.0	17.033955	7	7
84.0	17.040787	6	6
85.0	17.047221	5	5
86.0	17.05328	8	8
87.0	17.058985	10	10
88.0	17.064357	5	5
89.0	17.069417	5	5
90.0	17.074181	2	2
91.0	17.078668	3	3
92.0	17.082893	5	5
93.0	17.086871	5	5
94.0	17.090618	4	4
95.0	17.094146	6	6
96.0	17.097469	4	4
97.0	17.100598	2	2
98.0	17.103544	3	3
99.0	17.106319	5	5
100.0	17.108931	8	8
101.0	0	6	6
102.0	0	2	2
103.0	0	5	5
104.0	0	5	5
106.0	0	9	9
107.0	0	6	6
108.0	0	3	3
109.0	0	2	2
110.0	0	7	7
111.0	0	3	3
112.0	0	6	6
113.0	0	1	1
114.0	0	5	5
115.0	0	6	6
116.0	0	2	2
117.0	0	4	4
118.0	0	6	6
119.0	0	3	3
120.0	0	2	2
121.0	0	3	3
122.0	0	1	1
123.0	0	5	5
124.0	0	3	3
125.0	0	2	2
126.0	0	4	4
127.0	0	5	5
128.0	0	4	4
129.0	0	5	5
130.0	0	4	4
131.0	0	2	2
132.0	0	4	4
134.0	0	5	5
135.0	0	1	1
136.0	0	5	5
137.0	0	6	6
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	5	5
145.0	0	1	1
146.0	0	5	5
147.0	0	4	4
148.0	0	1	1
149.0	0	2	2
150.0	0	1	1
151.0	0	2	2
152.0	0	1	1
153.0	0	2	2
154.0	0	3	3
155.0	0	1	1
156.0	0	2	2
157.0	0	5	5
158.0	0	1	1
159.0	0	3	3
160.0	0	3	3
161.0	0	2	2
162.0	0	3	3
163.0	0	2	2
165.0	0	1	1
166.0	0	2	2
167.0	0	3	3
168.0	0	1	1
169.0	0	3	3
170.0	0	1	1
172.0	0	1	1
173.0	0	3	3
175.0	0	1	1
176.0	0	1	1
177.0	0	3	3
178.0	0	1	1
179.0	0	3	3
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	4	4
186.0	0	1	1
187.0	0	1	1
190.0	0	1	1
191.0	0	2	2
192.0	0	1	1
193.0	0	2	2
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	2	2
203.0	0	2	2
204.0	0	2	2
206.0	0	1	1
208.0	0	3	3
211.0	0	1	1
212.0	0	1	1
213.0	0	3	3
216.0	0	2	2
217.0	0	1	1
218.0	0	1	1
219.0	0	1	1
221.0	0	1	1
227.0	0	2	2
228.0	0	1	1
229.0	0	1	1
232.0	0	1	1
234.0	0	2	2
235.0	0	2	2
236.0	0	2	2
237.0	0	2	2
238.0	0	1	1
239.0	0	2	2
240.0	0	1	1
241.0	0	2	2
242.0	0	2	2
243.0	0	2	2
244.0	0	2	2
245.0	0	1	1
246.0	0	1	1
247.0	0	3	3
250.0	0	2	2
253.0	0	2	2
254.0	0	1	1
257.0	0	2	2
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	2	2
263.0	0	1	1
264.0	0	2	2
269.0	0	1	1
270.0	0	1	1
272.0	0	1	1
274.0	0	1	1
275.0	0	2	2
280.0	0	1	1
285.0	0	2	2
292.0	0	1	1
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
299.0	0	1	1
300.0	0	1	1
302.0	0	1	1
303.0	0	1	1
307.0	0	1	1
309.0	0	1	1
312.0	0	1	1
314.0	0	1	1
316.0	0	1	1
319.0	0	1	1
320.0	0	1	1
325.0	0	1	1
329.0	0	1	1
330.0	0	1	1
338.0	0	1	1
339.0	0	1	1
343.0	0	2	2
344.0	0	1	1
345.0	0	1	1
351.0	0	1	1
352.0	0	1	1
356.0	0	1	1
369.0	0	1	1
371.0	0	2	2
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
382.0	0	1	1
384.0	0	1	1
388.0	0	1	1
391.0	0	1	1
392.0	0	1	1
399.0	0	1	1
403.0	0	1	1
404.0	0	1	1
410.0	0	2	2
413.0	0	1	1
415.0	0	1	1
416.0	0	1	1
418.0	0	1	1
430.0	0	1	1
436.0	0	1	1
441.0	0	1	1
443.0	0	1	1
453.0	0	1	1
458.0	0	1	1
465.0	0	1	1
473.0	0	1	1
481.0	0	1	1
490.0	0	1	1
504.0	0	2	2
522.0	0	1	1
538.0	0	1	1
541.0	0	2	2
551.0	0	1	1
558.0	0	1	1
562.0	0	1	1
563.0	0	1	1
568.0	0	1	1
575.0	0	1	1
578.0	0	1	1
581.0	0	1	1
600.0	0	1	1
683.0	0	1	1
696.0	0	1	1
715.0	0	1	1
720.0	0	1	1
848.0	0	1	1
914.0	0	1	1
990.0	0	1	1