## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d09/VA_ch_18_m08d09.sorted_merged.bam] OUTPUT=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d09/VA_ch_18_m08d09.dedup.bam METRICS_FILE=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d09/VA_ch_18_m08d09.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: Mon Feb 15 19:53:42 UTC 2021

## 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	23689519	41311028	0	0	10629874	2902293	243082	0.154588	303277279

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005525	34951115	0	35167097
2.0	1.883001	2493415	239526	2302173
3.0	2.648735	141728	1751	118960
4.0	3.316956	9698	14	7896
5.0	3.900082	1642	3	1492
6.0	4.40895	778	0	772
7.0	4.853016	498	0	489
8.0	5.240532	397	0	401
9.0	5.5787	307	0	305
10.0	5.873804	234	0	232
11.0	6.131327	188	0	186
12.0	6.356056	139	0	138
13.0	6.552167	112	0	116
14.0	6.723304	114	0	112
15.0	6.872648	87	0	87
16.0	7.002973	82	0	80
17.0	7.116703	65	0	65
18.0	7.215949	46	0	48
19.0	7.302556	47	0	45
20.0	7.378135	43	0	45
21.0	7.444089	42	0	40
22.0	7.501644	30	0	30
23.0	7.55187	27	0	26
24.0	7.5957	18	0	17
25.0	7.633948	31	0	32
26.0	7.667325	27	0	26
27.0	7.696452	20	0	21
28.0	7.72187	19	0	20
29.0	7.744051	21	0	20
30.0	7.763407	19	0	19
31.0	7.780299	12	0	11
32.0	7.795039	12	0	12
33.0	7.807902	7	0	9
34.0	7.819127	12	0	13
35.0	7.828923	12	0	9
36.0	7.837471	8	0	9
37.0	7.844931	17	0	18
38.0	7.851441	14	0	14
39.0	7.857121	9	0	8
40.0	7.862079	8	0	7
41.0	7.866405	10	0	11
42.0	7.87018	2	0	2
43.0	7.873474	7	0	6
44.0	7.876349	12	0	13
45.0	7.878858	7	0	6
46.0	7.881047	12	0	12
47.0	7.882958	6	0	7
48.0	7.884625	9	0	8
49.0	7.88608	6	0	6
50.0	7.887349	8	0	8
51.0	7.888457	4	0	5
52.0	7.889424	9	0	10
53.0	7.890268	4	0	3
54.0	7.891004	6	0	5
55.0	7.891647	6	0	7
56.0	7.892207	5	0	5
57.0	7.892697	4	0	4
58.0	7.893124	4	0	4
59.0	7.893496	5	0	6
60.0	7.893821	9	0	7
61.0	7.894105	3	0	3
62.0	7.894353	6	0	6
63.0	7.894569	4	0	4
64.0	7.894757	1	0	1
65.0	7.894922	1	0	1
66.0	7.895066	4	0	5
67.0	7.895191	5	0	6
68.0	7.8953	5	0	3
69.0	7.895396	4	0	4
70.0	7.895479	1	0	1
71.0	7.895552	2	0	2
72.0	7.895615	2	0	2
73.0	7.89567	2	0	3
74.0	7.895719	6	0	6
75.0	7.895761	6	0	5
76.0	7.895798	3	0	4
77.0	7.89583	2	0	1
78.0	7.895858	4	0	6
79.0	7.895882	5	0	5
80.0	7.895904	4	0	2
81.0	7.895922	5	0	6
82.0	7.895938	1	0	2
83.0	7.895953	3	0	1
84.0	7.895965	0	0	0
85.0	7.895976	4	0	4
86.0	7.895985	1	0	5
87.0	7.895993	7	0	4
88.0	7.896001	2	0	4
89.0	7.896007	7	0	4
90.0	7.896012	1	0	1
91.0	7.896017	2	0	3
92.0	7.896021	3	0	2
93.0	7.896025	1	0	1
94.0	7.896028	5	0	6
95.0	7.896031	2	0	2
96.0	7.896033	2	0	1
97.0	7.896035	2	0	3
98.0	7.896037	2	0	1
99.0	7.896039	2	0	2
100.0	7.89604	1	0	2
101.0	0	3	0	2
102.0	0	1	0	1
103.0	0	2	0	3
104.0	0	8	0	7
105.0	0	3	0	3
106.0	0	1	0	1
107.0	0	2	0	2
109.0	0	0	0	1
110.0	0	2	0	1
111.0	0	1	0	1
112.0	0	1	0	1
114.0	0	1	0	1
115.0	0	2	0	2
116.0	0	1	0	1
119.0	0	1	0	1
120.0	0	1	0	1
121.0	0	1	0	1
122.0	0	3	0	3
123.0	0	2	0	2
125.0	0	2	0	4
126.0	0	3	0	1
129.0	0	1	0	1
133.0	0	2	0	2
135.0	0	1	0	2
136.0	0	3	0	2
137.0	0	1	0	1
141.0	0	1	0	3
142.0	0	2	0	0
143.0	0	1	0	2
144.0	0	1	0	0
147.0	0	1	0	1
148.0	0	0	0	1
149.0	0	1	0	0
151.0	0	0	0	1
152.0	0	1	0	0
153.0	0	1	0	2
154.0	0	1	0	0
159.0	0	0	0	1
160.0	0	2	0	2
161.0	0	1	0	1
162.0	0	1	0	0
170.0	0	1	0	1
177.0	0	1	0	2
178.0	0	1	0	1
179.0	0	1	0	0
180.0	0	2	0	2
181.0	0	1	0	1
182.0	0	1	0	2
183.0	0	1	0	0
185.0	0	1	0	2
186.0	0	2	0	1
189.0	0	0	0	1
190.0	0	1	0	0
191.0	0	1	0	1
192.0	0	0	0	1
193.0	0	1	0	1
194.0	0	2	0	1
195.0	0	1	0	1
196.0	0	0	0	1
197.0	0	1	0	0
198.0	0	1	0	1
201.0	0	2	0	2
203.0	0	3	0	3
206.0	0	1	0	1
209.0	0	1	0	1
210.0	0	1	0	1
212.0	0	1	0	1
216.0	0	1	0	1
220.0	0	1	0	1
221.0	0	1	0	1
224.0	0	1	0	1
229.0	0	1	0	2
230.0	0	1	0	0
231.0	0	1	0	1
237.0	0	1	0	1
240.0	0	1	0	1
242.0	0	1	0	1
250.0	0	0	0	1
253.0	0	1	0	0
255.0	0	1	0	2
256.0	0	1	0	0
258.0	0	1	0	1
262.0	0	0	0	1
264.0	0	1	0	0
269.0	0	1	0	1
274.0	0	1	0	1
276.0	0	1	0	1
277.0	0	0	0	1
278.0	0	1	0	0
286.0	0	1	0	2
288.0	0	1	0	1
290.0	0	1	0	0
294.0	0	1	0	1
298.0	0	0	0	1
299.0	0	1	0	0
314.0	0	1	0	1
315.0	0	1	0	1
318.0	0	0	0	1
319.0	0	1	0	0
321.0	0	1	0	1
333.0	0	0	0	1
334.0	0	1	0	0
353.0	0	1	0	1
356.0	0	1	0	1
371.0	0	1	0	1
372.0	0	1	0	1
376.0	0	0	0	1
377.0	0	1	0	0
382.0	0	1	0	1
429.0	0	1	0	1
430.0	0	0	0	1
431.0	0	1	0	0
432.0	0	0	0	1
433.0	0	1	0	0
435.0	0	0	0	1
436.0	0	1	0	0
440.0	0	1	0	1
441.0	0	0	0	1
442.0	0	1	0	0
446.0	0	0	0	1
448.0	0	1	0	0
470.0	0	2	0	2
495.0	0	0	0	1
496.0	0	1	0	0
520.0	0	0	0	1
521.0	0	1	0	0
531.0	0	0	0	1
532.0	0	1	0	0
622.0	0	0	0	1
624.0	0	1	0	0
631.0	0	1	0	1
672.0	0	0	0	1
673.0	0	0	0	1
674.0	0	1	0	0
675.0	0	1	0	0
705.0	0	0	0	1
706.0	0	2	0	1
912.0	0	0	0	1
916.0	0	1	0	0
1123.0	0	1	0	1
1143.0	0	0	0	1
1144.0	0	1	0	0
1441.0	0	0	0	1
1445.0	0	1	0	0