## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-08-31/TR_Ank_Yes_1_2014-08-31.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-08-31/TR_Ank_Yes_1_2014-08-31.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2014-08-31/TR_Ank_Yes_1_2014-08-31.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 08:34:09 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	2539316	18543198	0	0	508314	535291	0	0.039845	314969350

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17124918	17124918
2.0	1.942826	406168	406168
3.0	2.831748	9629	9629
4.0	3.669847	762	762
5.0	4.460029	352	352
6.0	5.205034	243	243
7.0	5.907443	205	205
8.0	6.569694	162	162
9.0	7.194082	140	140
10.0	7.782771	139	139
11.0	8.337802	123	123
12.0	8.861101	99	99
13.0	9.35448	75	75
14.0	9.819652	84	84
15.0	10.258228	83	83
16.0	10.671729	71	71
17.0	11.061588	51	51
18.0	11.429158	49	49
19.0	11.775713	59	59
20.0	12.102454	49	49
21.0	12.410514	41	41
22.0	12.700961	34	34
23.0	12.974803	44	44
24.0	13.232988	30	30
25.0	13.476411	33	33
26.0	13.705917	36	36
27.0	13.922302	28	28
28.0	14.126315	30	30
29.0	14.318663	30	30
30.0	14.500015	27	27
31.0	14.670998	15	15
32.0	14.832205	29	29
33.0	14.984196	14	14
34.0	15.127497	16	16
35.0	15.262605	16	16
36.0	15.389988	23	23
37.0	15.510088	22	22
38.0	15.623322	7	7
39.0	15.730081	29	29
40.0	15.830737	14	14
41.0	15.925638	13	13
42.0	16.015113	17	17
43.0	16.099473	19	19
44.0	16.179009	17	17
45.0	16.253998	12	12
46.0	16.3247	6	6
47.0	16.391359	11	11
48.0	16.454208	6	6
49.0	16.513463	7	7
50.0	16.56933	10	10
51.0	16.622003	16	16
52.0	16.671664	9	9
53.0	16.718487	11	11
54.0	16.762632	9	9
55.0	16.804253	8	8
56.0	16.843495	10	10
57.0	16.880493	9	9
58.0	16.915376	10	10
59.0	16.948264	8	8
60.0	16.979272	7	7
61.0	17.008507	6	6
62.0	17.036071	12	12
63.0	17.062059	14	14
64.0	17.086561	8	8
65.0	17.109662	7	7
66.0	17.131442	9	9
67.0	17.151978	3	3
68.0	17.171339	7	7
69.0	17.189593	11	11
70.0	17.206803	6	6
71.0	17.22303	8	8
72.0	17.238328	7	7
73.0	17.252752	9	9
74.0	17.266352	4	4
75.0	17.279174	8	8
76.0	17.291262	3	3
77.0	17.30266	4	4
78.0	17.313406	3	3
79.0	17.323538	10	10
80.0	17.33309	3	3
81.0	17.342096	3	3
82.0	17.350587	7	7
83.0	17.358593	2	2
84.0	17.366141	7	7
85.0	17.373258	3	3
86.0	17.379968	3	3
87.0	17.386294	6	6
88.0	17.392258	3	3
89.0	17.397881	4	4
90.0	17.403183	2	2
91.0	17.408182	7	7
92.0	17.412895	5	5
93.0	17.417338	3	3
94.0	17.421528	6	6
95.0	17.425478	9	9
96.0	17.429202	5	5
97.0	17.432713	7	7
98.0	17.436023	5	5
99.0	17.439144	2	2
100.0	17.442087	1	1
101.0	0	3	3
102.0	0	3	3
103.0	0	3	3
104.0	0	9	9
106.0	0	1	1
107.0	0	3	3
108.0	0	2	2
109.0	0	2	2
110.0	0	4	4
111.0	0	4	4
112.0	0	4	4
113.0	0	1	1
114.0	0	2	2
115.0	0	1	1
116.0	0	4	4
117.0	0	3	3
118.0	0	3	3
119.0	0	2	2
120.0	0	1	1
121.0	0	2	2
122.0	0	2	2
123.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	4	4
127.0	0	4	4
128.0	0	2	2
129.0	0	1	1
130.0	0	2	2
131.0	0	5	5
132.0	0	2	2
134.0	0	1	1
135.0	0	6	6
136.0	0	1	1
137.0	0	2	2
138.0	0	1	1
139.0	0	2	2
140.0	0	1	1
141.0	0	3	3
142.0	0	2	2
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	4	4
147.0	0	1	1
148.0	0	1	1
149.0	0	2	2
151.0	0	1	1
152.0	0	3	3
153.0	0	1	1
155.0	0	1	1
157.0	0	4	4
159.0	0	2	2
161.0	0	1	1
162.0	0	1	1
163.0	0	4	4
164.0	0	2	2
165.0	0	2	2
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	1	1
173.0	0	1	1
175.0	0	1	1
176.0	0	2	2
178.0	0	1	1
184.0	0	2	2
186.0	0	3	3
188.0	0	1	1
189.0	0	3	3
191.0	0	2	2
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	1	1
203.0	0	1	1
204.0	0	2	2
206.0	0	1	1
207.0	0	2	2
208.0	0	1	1
209.0	0	1	1
211.0	0	2	2
212.0	0	1	1
215.0	0	2	2
218.0	0	2	2
220.0	0	1	1
224.0	0	2	2
226.0	0	1	1
227.0	0	1	1
229.0	0	2	2
230.0	0	2	2
233.0	0	1	1
235.0	0	1	1
238.0	0	1	1
239.0	0	1	1
243.0	0	1	1
244.0	0	1	1
251.0	0	1	1
256.0	0	2	2
262.0	0	1	1
272.0	0	2	2
274.0	0	1	1
275.0	0	1	1
277.0	0	1	1
284.0	0	2	2
285.0	0	1	1
286.0	0	2	2
288.0	0	1	1
297.0	0	1	1
299.0	0	1	1
301.0	0	1	1
306.0	0	1	1
307.0	0	1	1
309.0	0	1	1
312.0	0	1	1
314.0	0	1	1
315.0	0	1	1
319.0	0	2	2
323.0	0	1	1
324.0	0	1	1
333.0	0	1	1
347.0	0	2	2
350.0	0	1	1
376.0	0	1	1
382.0	0	1	1
400.0	0	1	1
401.0	0	1	1
404.0	0	1	1
405.0	0	1	1
412.0	0	1	1
415.0	0	1	1
420.0	0	1	1
436.0	0	1	1
443.0	0	1	1
449.0	0	1	1
456.0	0	1	1
474.0	0	1	1
481.0	0	1	1
629.0	0	1	1
644.0	0	1	1
817.0	0	1	1