## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-10-05/CH_Vau_Cha_1_2014-10-05.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-10-05/CH_Vau_Cha_1_2014-10-05.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-10-05/CH_Vau_Cha_1_2014-10-05.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 08:24:20 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	2897545	17080036	0	0	540938	474486	0	0.040205	301694266

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15958938	15958938
2.0	1.944959	275291	275291
3.0	2.837907	5145	5145
4.0	3.681705	804	804
5.0	4.479061	479	479
6.0	5.232529	341	341
7.0	5.944525	245	245
8.0	6.617333	188	188
9.0	7.253108	148	148
10.0	7.85389	151	151
11.0	8.421604	113	113
12.0	8.958071	105	105
13.0	9.46501	91	91
14.0	9.944046	89	89
15.0	10.396716	73	73
16.0	10.824471	88	88
17.0	11.228681	66	66
18.0	11.610643	65	65
19.0	11.971582	61	61
20.0	12.312654	59	59
21.0	12.634954	58	58
22.0	12.939513	49	49
23.0	13.22731	50	50
24.0	13.499266	45	45
25.0	13.756253	41	41
26.0	13.999095	51	51
27.0	14.228571	32	32
28.0	14.445416	32	32
29.0	14.650326	43	43
30.0	14.843958	23	23
31.0	15.026932	19	19
32.0	15.199835	24	24
33.0	15.363221	28	28
34.0	15.517614	32	32
35.0	15.663509	29	29
36.0	15.801374	29	29
37.0	15.931651	21	21
38.0	16.054757	16	16
39.0	16.171088	20	20
40.0	16.281015	11	11
41.0	16.384892	20	20
42.0	16.483051	15	15
43.0	16.575808	21	21
44.0	16.663459	17	17
45.0	16.746286	15	15
46.0	16.824554	23	23
47.0	16.898514	18	18
48.0	16.968403	17	17
49.0	17.034445	8	8
50.0	17.096853	16	16
51.0	17.155825	12	12
52.0	17.211551	7	7
53.0	17.264211	15	15
54.0	17.313971	12	12
55.0	17.360993	13	13
56.0	17.405427	10	10
57.0	17.447415	15	15
58.0	17.487092	9	9
59.0	17.524586	17	17
60.0	17.560015	11	11
61.0	17.593494	17	17
62.0	17.625131	12	12
63.0	17.655027	8	8
64.0	17.683277	9	9
65.0	17.709972	6	6
66.0	17.735197	8	8
67.0	17.759034	7	7
68.0	17.78156	9	9
69.0	17.802845	8	8
70.0	17.822959	7	7
71.0	17.841966	14	14
72.0	17.859926	11	11
73.0	17.876898	7	7
74.0	17.892936	3	3
75.0	17.908091	12	12
76.0	17.922412	3	3
77.0	17.935945	6	6
78.0	17.948733	8	8
79.0	17.960817	3	3
80.0	17.972236	8	8
81.0	17.983026	6	6
82.0	17.993223	7	7
83.0	18.002858	9	9
84.0	18.011963	1	1
85.0	18.020567	11	11
86.0	18.028697	7	7
87.0	18.03638	5	5
88.0	18.04364	6	6
89.0	18.0505	6	6
90.0	18.056983	9	9
91.0	18.063108	10	10
92.0	18.068897	4	4
93.0	18.074367	4	4
94.0	18.079536	8	8
95.0	18.084421	6	6
96.0	18.089036	1	1
97.0	18.093398	5	5
98.0	18.097519	6	6
99.0	18.101414	4	4
100.0	18.105094	2	2
101.0	0	5	5
102.0	0	3	3
103.0	0	6	6
104.0	0	1	1
105.0	0	4	4
106.0	0	2	2
107.0	0	5	5
108.0	0	5	5
109.0	0	2	2
110.0	0	2	2
111.0	0	4	4
112.0	0	4	4
113.0	0	9	9
114.0	0	8	8
115.0	0	4	4
116.0	0	4	4
117.0	0	5	5
119.0	0	3	3
120.0	0	6	6
121.0	0	2	2
122.0	0	5	5
123.0	0	3	3
124.0	0	3	3
125.0	0	4	4
126.0	0	1	1
127.0	0	3	3
128.0	0	2	2
129.0	0	7	7
130.0	0	5	5
131.0	0	3	3
132.0	0	7	7
133.0	0	1	1
134.0	0	5	5
135.0	0	6	6
136.0	0	4	4
137.0	0	3	3
138.0	0	4	4
140.0	0	6	6
141.0	0	4	4
142.0	0	1	1
143.0	0	3	3
144.0	0	4	4
146.0	0	3	3
147.0	0	4	4
148.0	0	2	2
149.0	0	5	5
150.0	0	3	3
151.0	0	5	5
152.0	0	1	1
153.0	0	2	2
154.0	0	3	3
155.0	0	1	1
156.0	0	3	3
158.0	0	1	1
159.0	0	1	1
160.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
167.0	0	5	5
168.0	0	3	3
169.0	0	1	1
170.0	0	2	2
171.0	0	4	4
172.0	0	6	6
173.0	0	2	2
174.0	0	3	3
175.0	0	2	2
176.0	0	1	1
177.0	0	3	3
179.0	0	3	3
180.0	0	2	2
183.0	0	1	1
184.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	2	2
190.0	0	2	2
191.0	0	1	1
192.0	0	3	3
193.0	0	1	1
194.0	0	1	1
196.0	0	3	3
197.0	0	2	2
198.0	0	2	2
199.0	0	1	1
201.0	0	1	1
202.0	0	1	1
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
209.0	0	3	3
210.0	0	2	2
213.0	0	6	6
214.0	0	2	2
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
227.0	0	3	3
229.0	0	1	1
231.0	0	1	1
232.0	0	1	1
234.0	0	3	3
235.0	0	2	2
236.0	0	1	1
238.0	0	2	2
239.0	0	1	1
245.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	2	2
254.0	0	2	2
255.0	0	1	1
256.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	2	2
262.0	0	1	1
264.0	0	1	1
265.0	0	1	1
266.0	0	2	2
267.0	0	2	2
270.0	0	3	3
271.0	0	1	1
272.0	0	1	1
274.0	0	1	1
275.0	0	1	1
276.0	0	2	2
277.0	0	2	2
280.0	0	1	1
281.0	0	3	3
282.0	0	1	1
286.0	0	1	1
288.0	0	1	1
289.0	0	1	1
290.0	0	1	1
291.0	0	1	1
294.0	0	1	1
296.0	0	2	2
297.0	0	2	2
299.0	0	1	1
301.0	0	1	1
304.0	0	1	1
305.0	0	1	1
308.0	0	1	1
309.0	0	1	1
313.0	0	1	1
314.0	0	2	2
317.0	0	1	1
318.0	0	1	1
319.0	0	1	1
322.0	0	2	2
329.0	0	1	1
330.0	0	1	1
332.0	0	1	1
333.0	0	2	2
339.0	0	1	1
341.0	0	3	3
342.0	0	1	1
345.0	0	2	2
346.0	0	1	1
352.0	0	2	2
364.0	0	1	1
365.0	0	2	2
367.0	0	1	1
379.0	0	1	1
382.0	0	1	1
384.0	0	1	1
385.0	0	1	1
387.0	0	1	1
392.0	0	1	1
393.0	0	2	2
394.0	0	1	1
397.0	0	1	1
398.0	0	2	2
401.0	0	1	1
408.0	0	1	1
418.0	0	1	1
419.0	0	1	1
425.0	0	1	1
434.0	0	1	1
437.0	0	2	2
438.0	0	1	1
441.0	0	1	1
451.0	0	1	1
453.0	0	1	1
454.0	0	1	1
459.0	0	1	1
463.0	0	1	1
467.0	0	1	1
469.0	0	1	1
479.0	0	1	1
484.0	0	1	1
485.0	0	1	1
524.0	0	1	1
525.0	0	1	1
530.0	0	1	1
543.0	0	1	1
549.0	0	1	1
558.0	0	1	1
559.0	0	1	1
571.0	0	1	1
574.0	0	1	1
575.0	0	2	2
593.0	0	1	1
598.0	0	1	1
603.0	0	1	1
607.0	0	1	1
626.0	0	1	1
638.0	0	1	1
642.0	0	1	1
650.0	0	1	1
654.0	0	1	1
655.0	0	1	1
668.0	0	1	1
674.0	0	1	1
694.0	0	1	1
707.0	0	1	1
710.0	0	1	1
721.0	0	1	1
726.0	0	1	1
777.0	0	1	1
786.0	0	1	1
808.0	0	1	1
839.0	0	2	2
844.0	0	1	1
857.0	0	1	1
899.0	0	1	1
1044.0	0	1	1
1215.0	0	1	1
1412.0	0	1	1