## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_16_m09d02/VA_ch_16_m09d02.sorted_merged.bam] OUTPUT=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_16_m09d02/VA_ch_16_m09d02.dedup.bam METRICS_FILE=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_16_m09d02/VA_ch_16_m09d02.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 18:06:48 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	2899153	42384645	0	0	1179390	3745591	329318	0.098902	244639800

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007172	34562826	0	34845500
2.0	1.854128	3186940	323220	2946188
3.0	2.566354	232489	2988	194788
4.0	3.165282	17192	38	13344
5.0	3.668935	1788	2	1458
6.0	4.09247	506	0	478
7.0	4.448631	270	0	257
8.0	4.748135	207	0	209
9.0	4.999996	157	0	155
10.0	5.211791	117	0	117
11.0	5.389895	92	0	91
12.0	5.539668	86	0	87
13.0	5.665615	51	0	49
14.0	5.771527	45	0	46
15.0	5.860591	43	0	43
16.0	5.935487	36	0	36
17.0	5.998469	28	0	29
18.0	6.051432	28	0	27
19.0	6.09597	20	0	21
20.0	6.133423	26	0	24
21.0	6.164919	14	0	15
22.0	6.191404	10	0	11
23.0	6.213676	26	0	26
24.0	6.232405	13	0	12
25.0	6.248155	9	0	11
26.0	6.261399	10	0	10
27.0	6.272536	9	0	6
28.0	6.281902	9	0	9
29.0	6.289778	5	0	6
30.0	6.296401	10	0	10
31.0	6.301971	10	0	9
32.0	6.306654	4	0	4
33.0	6.310593	5	0	6
34.0	6.313905	6	0	6
35.0	6.31669	8	0	8
36.0	6.319032	3	0	3
37.0	6.321001	2	0	2
38.0	6.322658	9	0	8
39.0	6.32405	4	0	4
40.0	6.325221	2	0	2
41.0	6.326206	7	0	7
42.0	6.327035	5	0	5
43.0	6.327731	3	0	3
44.0	6.328317	5	0	5
45.0	6.328809	6	0	6
46.0	6.329223	4	0	4
47.0	6.329572	4	0	4
48.0	6.329865	1	0	1
49.0	6.330111	6	0	6
50.0	6.330318	4	0	5
51.0	6.330492	5	0	4
52.0	6.330639	1	0	3
53.0	6.330762	4	0	2
54.0	6.330865	2	0	3
55.0	6.330952	2	0	1
56.0	6.331026	2	0	2
57.0	6.331087	1	0	1
58.0	6.331139	1	0	2
59.0	6.331183	3	0	2
60.0	6.331219	2	0	2
61.0	6.33125	0	0	0
62.0	6.331276	2	0	3
63.0	6.331298	1	0	0
64.0	6.331316	0	0	0
65.0	6.331331	0	0	0
66.0	6.331344	2	0	2
67.0	6.331355	0	0	0
68.0	6.331364	2	0	2
69.0	6.331372	2	0	2
70.0	6.331379	0	0	0
71.0	6.331384	2	0	2
72.0	6.331389	1	0	1
73.0	6.331392	1	0	1
74.0	6.331396	2	0	2
75.0	6.331398	0	0	1
76.0	6.331401	1	0	1
77.0	6.331403	1	0	1
78.0	6.331404	0	0	1
79.0	6.331406	2	0	0
80.0	6.331407	1	0	1
81.0	6.331408	0	0	0
82.0	6.331408	1	0	1
83.0	6.331409	0	0	0
84.0	6.33141	1	0	1
85.0	6.33141	0	0	0
86.0	6.331411	1	0	1
87.0	6.331411	1	0	1
88.0	6.331411	0	0	1
89.0	6.331411	1	0	0
90.0	6.331412	0	0	0
91.0	6.331412	1	0	1
92.0	6.331412	0	0	0
93.0	6.331412	0	0	0
94.0	6.331412	1	0	1
95.0	6.331412	2	0	2
96.0	6.331412	0	0	0
97.0	6.331412	1	0	1
98.0	6.331413	0	0	0
99.0	6.331413	0	0	0
100.0	6.331413	1	0	1
101.0	0	2	0	2
103.0	0	1	0	1
105.0	0	1	0	1
106.0	0	1	0	1
110.0	0	1	0	1
124.0	0	0	0	1
126.0	0	2	0	1
131.0	0	1	0	1
138.0	0	1	0	1
139.0	0	0	0	1
140.0	0	1	0	0
142.0	0	1	0	1
153.0	0	1	0	1
155.0	0	1	0	1
168.0	0	1	0	2
169.0	0	1	0	0
174.0	0	1	0	1
176.0	0	0	0	1
177.0	0	1	0	0
178.0	0	0	0	1
179.0	0	1	0	0
184.0	0	0	0	1
185.0	0	1	0	0
193.0	0	1	0	1
197.0	0	1	0	1
206.0	0	1	0	1
207.0	0	1	0	1
216.0	0	0	0	1
217.0	0	1	0	1
218.0	0	2	0	1
222.0	0	0	0	1
223.0	0	1	0	0
226.0	0	1	0	1
228.0	0	1	0	1
229.0	0	1	0	1
231.0	0	0	0	1
232.0	0	1	0	0
234.0	0	1	0	1
237.0	0	1	0	1
243.0	0	1	0	1
246.0	0	1	0	1
248.0	0	1	0	1
266.0	0	1	0	1
268.0	0	1	0	1
270.0	0	0	0	1
272.0	0	1	0	0
273.0	0	1	0	1
275.0	0	1	0	1
292.0	0	0	0	1
293.0	0	1	0	0
303.0	0	0	0	1
304.0	0	2	0	2
305.0	0	1	0	0
314.0	0	0	0	1
316.0	0	1	0	0
344.0	0	1	0	1
365.0	0	1	0	1
387.0	0	1	0	1
403.0	0	1	0	1