## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-09-14/UA_Kha_Kha_1_2014-09-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-09-14/UA_Kha_Kha_1_2014-09-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-09-14/UA_Kha_Kha_1_2014-09-14.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 09:07:28 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	8082268	22040327	0	0	1981468	818640	0	0.069374	289303789

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20163265	20163265
2.0	1.926646	646680	646680
3.0	2.785318	20009	20009
4.0	3.581003	1138	1138
5.0	4.318321	361	361
6.0	5.001553	252	252
7.0	5.634668	215	215
8.0	6.22134	158	158
9.0	6.764978	156	156
10.0	7.268737	139	139
11.0	7.735544	133	133
12.0	8.168108	106	106
13.0	8.568942	91	91
14.0	8.940373	67	67
15.0	9.284558	76	76
16.0	9.603495	65	65
17.0	9.899037	47	47
18.0	10.1729	47	47
19.0	10.426674	58	58
20.0	10.661832	41	41
21.0	10.87974	41	41
22.0	11.081664	25	25
23.0	11.268776	46	46
24.0	11.442163	32	32
25.0	11.60283	40	40
26.0	11.751713	32	32
27.0	11.889673	26	26
28.0	12.017514	29	29
29.0	12.135978	23	23
30.0	12.245751	19	19
31.0	12.347472	20	20
32.0	12.441732	25	25
33.0	12.529077	30	30
34.0	12.610014	21	21
35.0	12.685015	19	19
36.0	12.754514	23	23
37.0	12.818915	23	23
38.0	12.878592	16	16
39.0	12.933892	22	22
40.0	12.985135	16	16
41.0	13.032619	21	21
42.0	13.07662	18	18
43.0	13.117393	12	12
44.0	13.155175	11	11
45.0	13.190186	14	14
46.0	13.222629	23	23
47.0	13.252692	11	11
48.0	13.280549	15	15
49.0	13.306364	7	7
50.0	13.330284	7	7
51.0	13.35245	10	10
52.0	13.37299	8	8
53.0	13.392023	11	11
54.0	13.40966	11	11
55.0	13.426003	11	11
56.0	13.441148	6	6
57.0	13.455181	7	7
58.0	13.468186	7	7
59.0	13.480236	15	15
60.0	13.491402	10	10
61.0	13.501749	8	8
62.0	13.511337	12	12
63.0	13.520222	5	5
64.0	13.528455	4	4
65.0	13.536084	9	9
66.0	13.543154	12	12
67.0	13.549705	9	9
68.0	13.555775	9	9
69.0	13.5614	4	4
70.0	13.566613	6	6
71.0	13.571443	5	5
72.0	13.575919	5	5
73.0	13.580066	9	9
74.0	13.58391	3	3
75.0	13.587471	8	8
76.0	13.590771	5	5
77.0	13.593829	8	8
78.0	13.596663	9	9
79.0	13.599289	5	5
80.0	13.601722	3	3
81.0	13.603977	5	5
82.0	13.606066	5	5
83.0	13.608002	4	4
84.0	13.609796	6	6
85.0	13.611459	6	6
86.0	13.612999	4	4
87.0	13.614427	6	6
88.0	13.615749	6	6
89.0	13.616975	6	6
90.0	13.618111	1	1
91.0	13.619164	4	4
92.0	13.620139	2	2
93.0	13.621043	3	3
94.0	13.62188	4	4
95.0	13.622656	5	5
96.0	13.623375	2	2
97.0	13.624042	3	3
98.0	13.624659	2	2
99.0	13.625231	4	4
100.0	13.625762	3	3
101.0	0	4	4
102.0	0	3	3
103.0	0	2	2
104.0	0	3	3
105.0	0	6	6
106.0	0	4	4
107.0	0	2	2
108.0	0	1	1
109.0	0	3	3
110.0	0	4	4
111.0	0	2	2
112.0	0	2	2
113.0	0	3	3
114.0	0	5	5
115.0	0	3	3
117.0	0	4	4
118.0	0	3	3
119.0	0	1	1
120.0	0	4	4
121.0	0	3	3
122.0	0	1	1
123.0	0	1	1
124.0	0	6	6
125.0	0	2	2
126.0	0	3	3
127.0	0	1	1
129.0	0	3	3
130.0	0	7	7
131.0	0	2	2
132.0	0	5	5
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	6	6
137.0	0	4	4
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
142.0	0	3	3
143.0	0	2	2
144.0	0	3	3
145.0	0	4	4
146.0	0	1	1
147.0	0	1	1
148.0	0	3	3
150.0	0	1	1
151.0	0	2	2
152.0	0	2	2
153.0	0	5	5
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
160.0	0	2	2
161.0	0	4	4
162.0	0	2	2
163.0	0	1	1
164.0	0	3	3
165.0	0	3	3
166.0	0	2	2
168.0	0	4	4
169.0	0	1	1
170.0	0	3	3
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	2	2
176.0	0	3	3
178.0	0	2	2
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	5	5
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
195.0	0	2	2
197.0	0	2	2
198.0	0	1	1
199.0	0	2	2
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
205.0	0	1	1
207.0	0	3	3
208.0	0	1	1
209.0	0	1	1
210.0	0	2	2
213.0	0	1	1
215.0	0	1	1
217.0	0	1	1
218.0	0	3	3
219.0	0	2	2
222.0	0	2	2
223.0	0	2	2
224.0	0	1	1
227.0	0	2	2
228.0	0	3	3
229.0	0	1	1
230.0	0	1	1
232.0	0	2	2
235.0	0	2	2
236.0	0	3	3
238.0	0	2	2
240.0	0	2	2
246.0	0	1	1
248.0	0	4	4
249.0	0	1	1
255.0	0	1	1
256.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	1	1
265.0	0	3	3
266.0	0	1	1
267.0	0	1	1
270.0	0	1	1
275.0	0	1	1
276.0	0	2	2
277.0	0	3	3
280.0	0	1	1
281.0	0	1	1
285.0	0	1	1
289.0	0	1	1
291.0	0	1	1
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
299.0	0	1	1
306.0	0	1	1
308.0	0	1	1
309.0	0	1	1
313.0	0	2	2
314.0	0	1	1
315.0	0	1	1
317.0	0	1	1
318.0	0	1	1
320.0	0	1	1
325.0	0	1	1
326.0	0	2	2
328.0	0	2	2
330.0	0	2	2
331.0	0	2	2
332.0	0	1	1
335.0	0	1	1
337.0	0	1	1
338.0	0	1	1
340.0	0	1	1
342.0	0	2	2
349.0	0	1	1
357.0	0	1	1
361.0	0	1	1
362.0	0	1	1
364.0	0	1	1
365.0	0	1	1
369.0	0	1	1
377.0	0	1	1
378.0	0	1	1
379.0	0	1	1
385.0	0	1	1
388.0	0	1	1
392.0	0	1	1
393.0	0	1	1
407.0	0	1	1
412.0	0	1	1
416.0	0	1	1
421.0	0	1	1
447.0	0	1	1
472.0	0	1	1
483.0	0	1	1
484.0	0	1	1
500.0	0	1	1
532.0	0	1	1
554.0	0	1	1
612.0	0	1	1
648.0	0	1	1
852.0	0	1	1