## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-07-20/AT_Nie_Mau_1_2014-07-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-07-20/AT_Nie_Mau_1_2014-07-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-07-20/AT_Nie_Mau_1_2014-07-20.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 09:11:06 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	2440531	26243002	0	0	645651	852899	0	0.042811	394941922

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	24072743	24072743
2.0	1.935712	729588	729588
3.0	2.811268	20089	20089
4.0	3.630537	969	969
5.0	4.397136	308	308
6.0	5.114452	243	243
7.0	5.785653	165	165
8.0	6.413704	153	153
9.0	7.001379	104	104
10.0	7.551273	98	98
11.0	8.065815	89	89
12.0	8.547278	89	89
13.0	8.997789	84	84
14.0	9.419338	61	61
15.0	9.813785	57	57
16.0	10.182875	46	46
17.0	10.528236	50	50
18.0	10.851395	42	42
19.0	11.153778	41	41
20.0	11.436722	39	39
21.0	11.701476	32	32
22.0	11.949209	26	26
23.0	12.181016	22	22
24.0	12.397921	24	24
25.0	12.600881	31	31
26.0	12.790793	32	32
27.0	12.968496	33	33
28.0	13.134775	32	32
29.0	13.290364	18	18
30.0	13.43595	18	18
31.0	13.572177	21	21
32.0	13.699646	21	21
33.0	13.818921	23	23
34.0	13.930527	20	20
35.0	14.034959	17	17
36.0	14.132677	15	15
37.0	14.224113	18	18
38.0	14.30967	8	8
39.0	14.389727	13	13
40.0	14.464638	9	9
41.0	14.534732	17	17
42.0	14.60032	10	10
43.0	14.661692	10	10
44.0	14.719119	10	10
45.0	14.772853	10	10
46.0	14.823133	8	8
47.0	14.87018	9	9
48.0	14.914203	12	12
49.0	14.955396	10	10
50.0	14.993941	11	11
51.0	15.030007	9	9
52.0	15.063755	12	12
53.0	15.095334	12	12
54.0	15.124882	8	8
55.0	15.152531	5	5
56.0	15.178402	7	7
57.0	15.20261	9	9
58.0	15.225261	12	12
59.0	15.246457	7	7
60.0	15.26629	3	3
61.0	15.284848	6	6
62.0	15.302212	6	6
63.0	15.318461	8	8
64.0	15.333664	4	4
65.0	15.347891	4	4
66.0	15.361203	7	7
67.0	15.373659	5	5
68.0	15.385314	5	5
69.0	15.39622	5	5
70.0	15.406425	5	5
71.0	15.415974	5	5
72.0	15.424908	10	10
73.0	15.433269	5	5
74.0	15.441092	1	1
75.0	15.448412	2	2
76.0	15.455261	5	5
77.0	15.461671	7	7
78.0	15.467668	2	2
79.0	15.473279	2	2
80.0	15.47853	6	6
81.0	15.483443	5	5
82.0	15.488041	6	6
83.0	15.492343	2	2
84.0	15.496368	4	4
85.0	15.500134	3	3
86.0	15.503659	6	6
87.0	15.506956	2	2
88.0	15.510042	6	6
89.0	15.51293	3	3
90.0	15.515631	5	5
91.0	15.518159	2	2
92.0	15.520525	4	4
93.0	15.522739	3	3
94.0	15.52481	1	1
95.0	15.526748	3	3
96.0	15.528561	3	3
97.0	15.530258	4	4
98.0	15.531846	3	3
99.0	15.533331	3	3
100.0	15.534722	3	3
101.0	0	6	6
102.0	0	3	3
103.0	0	6	6
104.0	0	7	7
105.0	0	1	1
106.0	0	2	2
107.0	0	2	2
108.0	0	4	4
109.0	0	3	3
110.0	0	2	2
111.0	0	3	3
112.0	0	2	2
113.0	0	3	3
114.0	0	1	1
116.0	0	1	1
118.0	0	1	1
119.0	0	2	2
121.0	0	1	1
122.0	0	3	3
123.0	0	2	2
125.0	0	3	3
126.0	0	1	1
127.0	0	2	2
133.0	0	3	3
134.0	0	1	1
135.0	0	1	1
136.0	0	4	4
137.0	0	1	1
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
141.0	0	3	3
142.0	0	2	2
143.0	0	2	2
144.0	0	3	3
145.0	0	1	1
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
150.0	0	1	1
151.0	0	1	1
154.0	0	1	1
155.0	0	3	3
157.0	0	1	1
159.0	0	1	1
160.0	0	1	1
162.0	0	1	1
163.0	0	2	2
164.0	0	3	3
166.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
179.0	0	1	1
180.0	0	2	2
181.0	0	1	1
184.0	0	1	1
186.0	0	1	1
188.0	0	1	1
189.0	0	2	2
195.0	0	2	2
196.0	0	2	2
197.0	0	1	1
198.0	0	1	1
202.0	0	1	1
203.0	0	1	1
205.0	0	2	2
207.0	0	1	1
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
213.0	0	1	1
217.0	0	1	1
218.0	0	1	1
219.0	0	1	1
226.0	0	2	2
228.0	0	1	1
241.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
249.0	0	1	1
251.0	0	1	1
253.0	0	1	1
259.0	0	1	1
260.0	0	1	1
264.0	0	1	1
267.0	0	1	1
271.0	0	1	1
274.0	0	1	1
275.0	0	1	1
276.0	0	1	1
279.0	0	1	1
282.0	0	1	1
285.0	0	1	1
293.0	0	1	1
297.0	0	2	2
304.0	0	1	1
310.0	0	1	1
322.0	0	1	1
326.0	0	1	1
329.0	0	1	1
335.0	0	1	1
353.0	0	1	1
363.0	0	1	1
366.0	0	1	1
419.0	0	1	1
429.0	0	1	1
504.0	0	1	1
601.0	0	1	1