## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d23/VA_ch_18_m08d23.sorted_merged.bam] OUTPUT=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d23/VA_ch_18_m08d23.dedup.bam METRICS_FILE=/scratch/yey2sn/DEST_example/pipeline_output/VA_ch_18_m08d23/VA_ch_18_m08d23.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 22:01:44 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	53132151	42365782	0	0	28222539	2768516	236690	0.244876	336321561

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005272	35770344	0	35983246
2.0	1.891563	2313923	233298	2122676
3.0	2.672955	118319	1634	98171
4.0	3.361864	7733	22	6323
5.0	3.969235	1643	2	1569
6.0	4.50472	933	6	928
7.0	4.976827	658	1	652
8.0	5.393056	491	2	487
9.0	5.760022	420	0	418
10.0	6.083555	351	0	353
11.0	6.368795	270	0	271
12.0	6.620276	226	0	221
13.0	6.841991	175	0	176
14.0	7.037465	168	0	169
15.0	7.209804	159	0	156
16.0	7.361745	164	0	168
17.0	7.495703	122	0	118
18.0	7.613805	112	0	116
19.0	7.71793	86	0	86
20.0	7.809731	103	0	98
21.0	7.890666	86	0	86
22.0	7.962022	76	0	76
23.0	8.024933	40	0	42
24.0	8.080398	68	0	70
25.0	8.129298	49	0	48
26.0	8.17241	56	0	53
27.0	8.21042	49	0	50
28.0	8.243931	43	0	41
29.0	8.273476	34	0	38
30.0	8.299524	41	0	40
31.0	8.322489	28	0	29
32.0	8.342736	29	0	29
33.0	8.360586	34	0	32
34.0	8.376324	27	0	28
35.0	8.390199	31	0	29
36.0	8.402432	29	0	30
37.0	8.413217	22	0	22
38.0	8.422726	27	0	26
39.0	8.431109	24	0	24
40.0	8.4385	16	0	14
41.0	8.445016	9	0	12
42.0	8.450761	20	0	18
43.0	8.455826	14	0	18
44.0	8.460291	15	0	14
45.0	8.464228	17	0	14
46.0	8.467699	11	0	14
47.0	8.47076	11	0	9
48.0	8.473458	11	0	10
49.0	8.475836	11	0	10
50.0	8.477933	8	0	8
51.0	8.479782	7	0	9
52.0	8.481412	7	0	8
53.0	8.48285	9	0	11
54.0	8.484117	14	0	11
55.0	8.485234	12	0	11
56.0	8.486219	11	0	13
57.0	8.487087	14	0	14
58.0	8.487853	8	0	5
59.0	8.488527	10	0	12
60.0	8.489123	6	0	8
61.0	8.489647	7	0	5
62.0	8.49011	11	0	10
63.0	8.490517	9	0	10
64.0	8.490877	11	0	11
65.0	8.491194	10	0	8
66.0	8.491473	5	0	9
67.0	8.49172	5	0	2
68.0	8.491937	7	0	8
69.0	8.492129	7	0	6
70.0	8.492297	8	0	8
71.0	8.492446	5	0	5
72.0	8.492577	7	0	6
73.0	8.492693	4	0	4
74.0	8.492795	1	0	2
75.0	8.492885	3	0	3
76.0	8.492964	2	0	3
77.0	8.493034	9	0	9
78.0	8.493096	6	0	7
79.0	8.49315	7	0	5
80.0	8.493198	4	0	6
81.0	8.49324	5	0	3
82.0	8.493278	6	0	7
83.0	8.493311	3	0	2
84.0	8.493339	4	0	4
85.0	8.493365	6	0	5
86.0	8.493388	2	0	3
87.0	8.493407	4	0	4
88.0	8.493425	4	0	5
89.0	8.49344	7	0	6
90.0	8.493454	2	0	1
91.0	8.493466	3	0	3
92.0	8.493476	0	0	0
93.0	8.493486	3	0	5
94.0	8.493494	4	0	2
95.0	8.493501	2	0	2
96.0	8.493508	3	0	3
97.0	8.493513	2	0	2
98.0	8.493518	0	0	0
99.0	8.493523	1	0	1
100.0	8.493526	1	0	1
101.0	0	5	0	5
102.0	0	3	0	5
103.0	0	6	0	6
104.0	0	4	0	5
105.0	0	5	0	5
106.0	0	2	0	3
107.0	0	6	0	4
108.0	0	4	0	2
109.0	0	4	0	5
110.0	0	3	0	2
111.0	0	2	0	4
112.0	0	3	0	1
113.0	0	2	0	3
114.0	0	7	0	7
115.0	0	3	0	4
116.0	0	4	0	2
117.0	0	4	0	6
118.0	0	2	0	2
119.0	0	2	0	0
120.0	0	3	0	3
121.0	0	2	0	3
122.0	0	4	0	5
123.0	0	2	0	1
124.0	0	1	0	1
125.0	0	3	0	3
126.0	0	1	0	1
127.0	0	0	0	1
128.0	0	2	0	2
129.0	0	3	0	4
130.0	0	3	0	1
131.0	0	3	0	5
132.0	0	5	0	4
133.0	0	5	0	6
134.0	0	2	0	1
135.0	0	3	0	1
137.0	0	2	0	2
138.0	0	2	0	2
139.0	0	3	0	4
140.0	0	1	0	0
143.0	0	4	0	8
144.0	0	5	0	2
145.0	0	2	0	1
147.0	0	1	0	1
149.0	0	0	0	1
150.0	0	1	0	2
151.0	0	4	0	2
152.0	0	2	0	4
153.0	0	2	0	3
154.0	0	3	0	0
155.0	0	2	0	3
156.0	0	1	0	0
158.0	0	1	0	2
159.0	0	1	0	3
160.0	0	3	0	2
161.0	0	4	0	2
162.0	0	1	0	1
163.0	0	1	0	1
164.0	0	1	0	3
165.0	0	1	0	1
166.0	0	3	0	1
167.0	0	0	0	1
168.0	0	1	0	1
169.0	0	1	0	0
170.0	0	2	0	2
172.0	0	0	0	2
173.0	0	2	0	0
175.0	0	0	0	1
176.0	0	2	0	1
177.0	0	2	0	2
180.0	0	1	0	1
181.0	0	1	0	2
182.0	0	1	0	0
183.0	0	0	0	2
184.0	0	1	0	1
185.0	0	2	0	1
186.0	0	1	0	0
188.0	0	1	0	2
189.0	0	2	0	2
190.0	0	1	0	0
191.0	0	0	0	1
192.0	0	0	0	1
193.0	0	3	0	1
197.0	0	1	0	4
198.0	0	4	0	1
199.0	0	2	0	3
200.0	0	1	0	0
201.0	0	2	0	3
202.0	0	2	0	3
203.0	0	2	0	1
204.0	0	1	0	1
205.0	0	1	0	0
206.0	0	1	0	1
207.0	0	1	0	1
208.0	0	2	0	2
211.0	0	1	0	2
212.0	0	2	0	1
214.0	0	0	0	1
216.0	0	2	0	2
217.0	0	1	0	0
218.0	0	0	0	1
220.0	0	0	0	1
221.0	0	1	0	1
222.0	0	1	0	1
223.0	0	2	0	2
224.0	0	1	0	0
225.0	0	1	0	1
226.0	0	2	0	3
227.0	0	1	0	1
228.0	0	2	0	1
229.0	0	1	0	0
230.0	0	1	0	1
231.0	0	0	0	1
234.0	0	1	0	1
237.0	0	1	0	0
238.0	0	0	0	2
239.0	0	2	0	1
240.0	0	2	0	1
243.0	0	1	0	3
244.0	0	2	0	0
246.0	0	2	0	2
248.0	0	1	0	1
252.0	0	1	0	1
253.0	0	0	0	1
254.0	0	1	0	0
255.0	0	0	0	1
256.0	0	2	0	2
257.0	0	1	0	0
259.0	0	1	0	1
261.0	0	0	0	2
262.0	0	1	0	0
265.0	0	2	0	2
267.0	0	1	0	0
269.0	0	0	0	1
271.0	0	1	0	0
272.0	0	1	0	1
274.0	0	0	0	1
275.0	0	2	0	1
276.0	0	1	0	1
278.0	0	1	0	1
279.0	0	1	0	1
280.0	0	1	0	1
284.0	0	1	0	1
294.0	0	0	0	1
295.0	0	1	0	0
298.0	0	0	0	1
299.0	0	1	0	0
305.0	0	1	0	1
307.0	0	1	0	1
308.0	0	0	0	1
309.0	0	2	0	1
322.0	0	1	0	1
324.0	0	0	0	1
325.0	0	1	0	0
329.0	0	0	0	1
331.0	0	1	0	1
333.0	0	1	0	0
337.0	0	3	0	3
343.0	0	0	0	1
344.0	0	1	0	0
346.0	0	0	0	1
347.0	0	1	0	0
349.0	0	1	0	1
356.0	0	1	0	1
357.0	0	1	0	1
361.0	0	1	0	1
367.0	0	0	0	1
368.0	0	1	0	0
372.0	0	1	0	1
376.0	0	1	0	1
394.0	0	0	0	1
395.0	0	1	0	0
396.0	0	0	0	1
397.0	0	1	0	0
399.0	0	0	0	1
400.0	0	1	0	0
403.0	0	0	0	1
404.0	0	0	0	1
405.0	0	2	0	0
407.0	0	0	0	1
408.0	0	1	0	0
439.0	0	1	0	2
440.0	0	1	0	0
458.0	0	1	0	1
505.0	0	0	0	1
506.0	0	1	0	0
522.0	0	0	0	1
523.0	0	1	0	0
530.0	0	1	0	1
559.0	0	1	0	1
590.0	0	0	0	1
592.0	0	1	0	0
609.0	0	0	0	1
610.0	0	1	0	0
712.0	0	0	0	1
713.0	0	1	0	0
716.0	0	0	0	1
718.0	0	1	0	0
944.0	0	0	0	1
946.0	0	1	0	0
1015.0	0	0	0	1
1018.0	0	1	0	0
1192.0	0	0	0	1
1197.0	0	1	0	0
1272.0	0	0	0	1
1273.0	0	1	0	0
1496.0	0	0	0	1
1498.0	0	1	0	0
1531.0	0	0	0	1
1536.0	0	1	0	0
1538.0	0	0	0	1
1541.0	0	1	0	0
1599.0	0	0	0	1
1601.0	0	1	0	0
1684.0	0	0	0	1
1691.0	0	1	0	0
1740.0	0	0	0	1
1744.0	0	1	0	0
1830.0	0	0	0	1
1832.0	0	1	0	0
1846.0	0	1	0	1
1876.0	0	0	0	1
1881.0	0	1	0	0
1917.0	0	0	0	1
1919.0	0	1	0	0
1935.0	0	1	0	1
2029.0	0	0	0	1
2031.0	0	1	0	0
2105.0	0	0	0	1
2110.0	0	1	0	0
2208.0	0	0	0	1
2214.0	0	1	0	0
2258.0	0	0	0	1
2261.0	0	1	0	0
2520.0	0	0	0	1
2525.0	0	1	0	0
3050.0	0	0	0	2
3052.0	0	1	0	0
3053.0	0	1	0	0
3294.0	0	0	0	1
3301.0	0	1	0	0