## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Mar_1_2014-10-20/GB_Lei_Mar_1_2014-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Mar_1_2014-10-20/GB_Lei_Mar_1_2014-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Lei_Mar_1_2014-10-20/GB_Lei_Mar_1_2014-10-20.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 08:50:13 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	7585832	31520153	0	0	2187282	898194	0	0.056405	542508008

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	29455849	29455849
2.0	1.943555	726435	726435
3.0	2.833851	14036	14036
4.0	3.673893	806	806
5.0	4.46652	392	392
6.0	5.214406	279	279
7.0	5.920078	213	213
8.0	6.585918	196	196
9.0	7.214175	167	167
10.0	7.80697	148	148
11.0	8.366304	109	109
12.0	8.894066	153	153
13.0	9.392039	112	112
14.0	9.861904	109	109
15.0	10.305247	114	114
16.0	10.723566	93	93
17.0	11.118272	91	91
18.0	11.490699	83	83
19.0	11.842105	60	60
20.0	12.173675	59	59
21.0	12.48653	53	53
22.0	12.781726	53	53
23.0	13.060259	51	51
24.0	13.32307	48	48
25.0	13.571047	41	41
26.0	13.805027	30	30
27.0	14.0258	46	46
28.0	14.234111	30	30
29.0	14.430664	40	40
30.0	14.616123	42	42
31.0	14.791113	44	44
32.0	14.956226	28	28
33.0	15.11202	31	31
34.0	15.259019	17	17
35.0	15.397721	25	25
36.0	15.528594	30	30
37.0	15.65208	30	30
38.0	15.768595	21	21
39.0	15.878534	20	20
40.0	15.982268	20	20
41.0	16.080146	19	19
42.0	16.172499	19	19
43.0	16.25964	19	19
44.0	16.341861	20	20
45.0	16.419442	23	23
46.0	16.492644	11	11
47.0	16.561714	12	12
48.0	16.626885	11	11
49.0	16.688378	16	16
50.0	16.746399	13	13
51.0	16.801146	17	17
52.0	16.852802	19	19
53.0	16.901543	15	15
54.0	16.947532	14	14
55.0	16.990926	12	12
56.0	17.03187	14	14
57.0	17.070503	10	10
58.0	17.106956	12	12
59.0	17.141351	13	13
60.0	17.173804	16	16
61.0	17.204426	10	10
62.0	17.233319	3	3
63.0	17.260581	11	11
64.0	17.286305	16	16
65.0	17.310576	6	6
66.0	17.333478	13	13
67.0	17.355087	5	5
68.0	17.375476	6	6
69.0	17.394714	7	7
70.0	17.412866	9	9
71.0	17.429994	4	4
72.0	17.446155	9	9
73.0	17.461404	12	12
74.0	17.475792	6	6
75.0	17.489368	4	4
76.0	17.502177	8	8
77.0	17.514264	5	5
78.0	17.525668	5	5
79.0	17.536429	4	4
80.0	17.546582	6	6
81.0	17.556162	1	1
82.0	17.565201	2	2
83.0	17.573731	6	6
84.0	17.581778	5	5
85.0	17.589372	8	8
86.0	17.596537	7	7
87.0	17.603297	6	6
88.0	17.609676	5	5
89.0	17.615695	3	3
90.0	17.621374	2	2
91.0	17.626732	3	3
92.0	17.631788	10	10
93.0	17.636559	3	3
94.0	17.64106	5	5
95.0	17.645308	7	7
96.0	17.649315	1	1
97.0	17.653096	5	5
98.0	17.656664	5	5
99.0	17.660031	2	2
100.0	17.663207	5	5
101.0	0	4	4
102.0	0	3	3
103.0	0	2	2
104.0	0	2	2
105.0	0	6	6
106.0	0	2	2
107.0	0	6	6
108.0	0	2	2
109.0	0	2	2
110.0	0	5	5
111.0	0	3	3
112.0	0	4	4
113.0	0	4	4
114.0	0	3	3
115.0	0	3	3
118.0	0	1	1
119.0	0	3	3
120.0	0	3	3
121.0	0	6	6
122.0	0	1	1
123.0	0	3	3
124.0	0	1	1
126.0	0	3	3
127.0	0	2	2
128.0	0	1	1
129.0	0	3	3
130.0	0	1	1
132.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	3	3
137.0	0	2	2
138.0	0	1	1
140.0	0	3	3
141.0	0	2	2
142.0	0	3	3
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	4	4
147.0	0	4	4
149.0	0	3	3
150.0	0	1	1
151.0	0	1	1
152.0	0	2	2
153.0	0	3	3
154.0	0	1	1
155.0	0	1	1
156.0	0	4	4
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	2	2
166.0	0	3	3
167.0	0	2	2
168.0	0	1	1
170.0	0	3	3
171.0	0	4	4
172.0	0	2	2
173.0	0	3	3
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
180.0	0	1	1
182.0	0	4	4
183.0	0	2	2
185.0	0	1	1
186.0	0	2	2
187.0	0	2	2
188.0	0	2	2
189.0	0	1	1
190.0	0	1	1
192.0	0	1	1
194.0	0	2	2
195.0	0	1	1
196.0	0	3	3
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
206.0	0	2	2
208.0	0	1	1
209.0	0	1	1
210.0	0	2	2
211.0	0	2	2
212.0	0	3	3
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
217.0	0	1	1
218.0	0	2	2
220.0	0	1	1
221.0	0	2	2
222.0	0	2	2
223.0	0	3	3
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
236.0	0	1	1
237.0	0	2	2
239.0	0	2	2
240.0	0	1	1
242.0	0	1	1
244.0	0	2	2
247.0	0	1	1
248.0	0	2	2
255.0	0	1	1
256.0	0	1	1
257.0	0	2	2
261.0	0	1	1
263.0	0	3	3
264.0	0	1	1
265.0	0	1	1
267.0	0	1	1
268.0	0	1	1
270.0	0	2	2
271.0	0	1	1
274.0	0	3	3
276.0	0	1	1
277.0	0	1	1
278.0	0	1	1
279.0	0	2	2
283.0	0	1	1
285.0	0	1	1
286.0	0	3	3
288.0	0	1	1
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	2	2
294.0	0	2	2
295.0	0	2	2
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
305.0	0	1	1
311.0	0	1	1
313.0	0	2	2
316.0	0	1	1
320.0	0	1	1
325.0	0	1	1
332.0	0	1	1
335.0	0	1	1
338.0	0	1	1
345.0	0	2	2
349.0	0	1	1
357.0	0	1	1
367.0	0	1	1
371.0	0	2	2
375.0	0	1	1
383.0	0	1	1
393.0	0	1	1
395.0	0	1	1
396.0	0	1	1
399.0	0	2	2
401.0	0	1	1
405.0	0	1	1
414.0	0	1	1
415.0	0	1	1
417.0	0	1	1
421.0	0	1	1
430.0	0	2	2
433.0	0	1	1
438.0	0	1	1
443.0	0	1	1
446.0	0	1	1
454.0	0	1	1
480.0	0	2	2
482.0	0	2	2
486.0	0	1	1
561.0	0	1	1
629.0	0	1	1
664.0	0	1	1
680.0	0	1	1