## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_She_She_1_2014-08-25/GB_She_She_1_2014-08-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_She_She_1_2014-08-25/GB_She_She_1_2014-08-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_She_She_1_2014-08-25/GB_She_She_1_2014-08-25.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 10:20:29 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	3261324	43096771	0	0	1200965	1461660	0	0.046105	620901809

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	39464602	39464602
2.0	1.932944	1221207	1221207
3.0	2.803329	34010	34010
4.0	3.615349	1721	1721
5.0	4.372919	485	485
6.0	5.079689	311	311
7.0	5.739066	234	234
8.0	6.354228	204	204
9.0	6.92814	162	162
10.0	7.463567	120	120
11.0	7.963091	127	127
12.0	8.429119	101	101
13.0	8.863897	99	99
14.0	9.269521	97	97
15.0	9.647945	91	91
16.0	10.000994	72	72
17.0	10.330368	70	70
18.0	10.637657	63	63
19.0	10.924339	45	45
20.0	11.191798	45	45
21.0	11.441322	52	52
22.0	11.674115	51	51
23.0	11.891297	45	45
24.0	12.093915	40	40
25.0	12.282947	42	42
26.0	12.459304	38	38
27.0	12.623834	45	45
28.0	12.777332	19	19
29.0	12.920537	21	21
30.0	13.054139	22	22
31.0	13.178782	24	24
32.0	13.295068	32	32
33.0	13.403555	21	21
34.0	13.504768	24	24
35.0	13.599194	19	19
36.0	13.687289	25	25
37.0	13.769475	25	25
38.0	13.846151	23	23
39.0	13.917686	17	17
40.0	13.984423	19	19
41.0	14.046685	13	13
42.0	14.104773	27	27
43.0	14.158965	16	16
44.0	14.209523	19	19
45.0	14.256691	17	17
46.0	14.300696	13	13
47.0	14.341751	24	24
48.0	14.380052	16	16
49.0	14.415785	13	13
50.0	14.449122	13	13
51.0	14.480224	16	16
52.0	14.50924	12	12
53.0	14.53631	13	13
54.0	14.561565	16	16
55.0	14.585127	9	9
56.0	14.607108	15	15
57.0	14.627616	16	16
58.0	14.646749	9	9
59.0	14.664598	8	8
60.0	14.681251	11	11
61.0	14.696787	9	9
62.0	14.711281	7	7
63.0	14.724803	3	3
64.0	14.737419	10	10
65.0	14.749188	9	9
66.0	14.760169	12	12
67.0	14.770413	15	15
68.0	14.77997	9	9
69.0	14.788886	10	10
70.0	14.797204	15	15
71.0	14.804965	3	3
72.0	14.812205	6	6
73.0	14.81896	9	9
74.0	14.825262	7	7
75.0	14.831141	10	10
76.0	14.836626	11	11
77.0	14.841743	5	5
78.0	14.846517	5	5
79.0	14.850971	5	5
80.0	14.855126	3	3
81.0	14.859003	8	8
82.0	14.862619	5	5
83.0	14.865993	6	6
84.0	14.869141	5	5
85.0	14.872078	4	4
86.0	14.874818	5	5
87.0	14.877374	7	7
88.0	14.879759	7	7
89.0	14.881984	3	3
90.0	14.884059	2	2
91.0	14.885996	2	2
92.0	14.887802	1	1
93.0	14.889488	3	3
94.0	14.89106	9	9
95.0	14.892527	2	2
96.0	14.893896	6	6
97.0	14.895173	5	5
98.0	14.896364	7	7
99.0	14.897475	10	10
100.0	14.898512	5	5
101.0	0	4	4
102.0	0	3	3
103.0	0	6	6
104.0	0	7	7
105.0	0	5	5
106.0	0	4	4
107.0	0	6	6
108.0	0	5	5
109.0	0	4	4
110.0	0	4	4
111.0	0	2	2
112.0	0	3	3
113.0	0	1	1
114.0	0	2	2
115.0	0	10	10
116.0	0	2	2
117.0	0	1	1
118.0	0	2	2
119.0	0	4	4
120.0	0	3	3
121.0	0	4	4
122.0	0	4	4
123.0	0	7	7
124.0	0	3	3
125.0	0	5	5
126.0	0	1	1
127.0	0	2	2
129.0	0	1	1
130.0	0	4	4
131.0	0	4	4
132.0	0	3	3
133.0	0	2	2
134.0	0	5	5
135.0	0	4	4
136.0	0	3	3
137.0	0	1	1
138.0	0	1	1
139.0	0	5	5
140.0	0	4	4
141.0	0	7	7
142.0	0	2	2
143.0	0	2	2
144.0	0	3	3
145.0	0	2	2
146.0	0	2	2
147.0	0	2	2
148.0	0	3	3
150.0	0	5	5
151.0	0	2	2
153.0	0	2	2
154.0	0	4	4
155.0	0	2	2
156.0	0	2	2
158.0	0	3	3
159.0	0	1	1
162.0	0	2	2
163.0	0	2	2
164.0	0	1	1
165.0	0	3	3
166.0	0	2	2
167.0	0	1	1
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
173.0	0	2	2
174.0	0	2	2
176.0	0	2	2
178.0	0	3	3
179.0	0	4	4
180.0	0	3	3
181.0	0	3	3
183.0	0	1	1
184.0	0	1	1
186.0	0	3	3
187.0	0	2	2
188.0	0	1	1
189.0	0	3	3
190.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
196.0	0	2	2
197.0	0	4	4
198.0	0	6	6
199.0	0	1	1
200.0	0	3	3
204.0	0	2	2
205.0	0	3	3
206.0	0	1	1
209.0	0	2	2
213.0	0	1	1
215.0	0	2	2
216.0	0	2	2
217.0	0	2	2
218.0	0	2	2
219.0	0	2	2
221.0	0	1	1
226.0	0	1	1
227.0	0	1	1
229.0	0	1	1
231.0	0	4	4
232.0	0	1	1
234.0	0	3	3
235.0	0	1	1
237.0	0	2	2
238.0	0	1	1
240.0	0	4	4
241.0	0	1	1
243.0	0	2	2
244.0	0	1	1
245.0	0	1	1
247.0	0	2	2
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
252.0	0	2	2
253.0	0	1	1
254.0	0	2	2
255.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
262.0	0	2	2
271.0	0	1	1
272.0	0	2	2
273.0	0	1	1
277.0	0	1	1
280.0	0	1	1
281.0	0	2	2
285.0	0	2	2
287.0	0	1	1
288.0	0	1	1
289.0	0	1	1
290.0	0	2	2
291.0	0	1	1
294.0	0	1	1
296.0	0	1	1
297.0	0	3	3
298.0	0	1	1
299.0	0	2	2
300.0	0	1	1
312.0	0	1	1
315.0	0	1	1
318.0	0	1	1
320.0	0	1	1
322.0	0	1	1
327.0	0	1	1
328.0	0	1	1
329.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
339.0	0	2	2
342.0	0	1	1
347.0	0	1	1
350.0	0	1	1
356.0	0	1	1
359.0	0	1	1
361.0	0	1	1
362.0	0	1	1
364.0	0	1	1
367.0	0	1	1
370.0	0	1	1
371.0	0	1	1
373.0	0	2	2
377.0	0	1	1
383.0	0	1	1
384.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	1	1
389.0	0	1	1
390.0	0	1	1
419.0	0	1	1
426.0	0	1	1
430.0	0	1	1
431.0	0	1	1
440.0	0	1	1
441.0	0	1	1
446.0	0	1	1
459.0	0	1	1
475.0	0	1	1
480.0	0	1	1
481.0	0	1	1
484.0	0	2	2
488.0	0	1	1
492.0	0	1	1
493.0	0	1	1
495.0	0	1	1
500.0	0	1	1
508.0	0	1	1
512.0	0	2	2
514.0	0	1	1
517.0	0	1	1
521.0	0	1	1
524.0	0	1	1
532.0	0	1	1
569.0	0	1	1
574.0	0	1	1
592.0	0	1	1
596.0	0	1	1
605.0	0	2	2
613.0	0	1	1
623.0	0	1	1
639.0	0	1	1
663.0	0	1	1
694.0	0	1	1
707.0	0	1	1
715.0	0	1	1
728.0	0	1	1
741.0	0	1	1
750.0	0	1	1
807.0	0	1	1
889.0	0	1	1
1059.0	0	1	1
1090.0	0	1	1