## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-10-13/TR_Ank_Yes_1_2016-10-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-10-13/TR_Ank_Yes_1_2016-10-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-10-13/TR_Ank_Yes_1_2016-10-13.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 08:40:29 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	25134496	7012671	0	0	5420420	578764	0	0.167977	40113771

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	5850648	5850648
2.0	1.839609	348865	348865
3.0	2.544551	26277	26277
4.0	3.136427	3567	3567
5.0	3.633371	1428	1428
6.0	4.050609	824	824
7.0	4.400926	557	557
8.0	4.695055	428	428
9.0	4.942008	350	350
10.0	5.149352	259	259
11.0	5.32344	205	205
12.0	5.469605	200	200
13.0	5.592327	181	181
14.0	5.695366	149	149
15.0	5.781878	147	147
16.0	5.854514	129	129
17.0	5.9155	123	123
18.0	5.966704	122	122
19.0	6.009695	135	135
20.0	6.045791	107	107
21.0	6.076098	104	104
22.0	6.101544	75	75
23.0	6.122908	67	67
24.0	6.140846	72	72
25.0	6.155906	65	65
26.0	6.168552	68	68
27.0	6.179168	53	53
28.0	6.188082	63	63
29.0	6.195567	60	60
30.0	6.201851	50	50
31.0	6.207127	49	49
32.0	6.211556	28	28
33.0	6.215276	39	39
34.0	6.218398	35	35
35.0	6.22102	29	29
36.0	6.223222	34	34
37.0	6.22507	27	27
38.0	6.226622	30	30
39.0	6.227925	27	27
40.0	6.229019	19	19
41.0	6.229937	24	24
42.0	6.230708	21	21
43.0	6.231356	21	21
44.0	6.231899	20	20
45.0	6.232356	20	20
46.0	6.232739	23	23
47.0	6.233061	16	16
48.0	6.233331	16	16
49.0	6.233558	20	20
50.0	6.233748	22	22
51.0	6.233908	9	9
52.0	6.234042	13	13
53.0	6.234155	19	19
54.0	6.23425	14	14
55.0	6.234329	13	13
56.0	6.234396	22	22
57.0	6.234452	12	12
58.0	6.234499	15	15
59.0	6.234539	9	9
60.0	6.234572	14	14
61.0	6.2346	19	19
62.0	6.234623	14	14
63.0	6.234643	9	9
64.0	6.234659	11	11
65.0	6.234673	7	7
66.0	6.234684	16	16
67.0	6.234694	9	9
68.0	6.234702	13	13
69.0	6.234709	4	4
70.0	6.234715	11	11
71.0	6.23472	7	7
72.0	6.234724	8	8
73.0	6.234727	11	11
74.0	6.23473	12	12
75.0	6.234733	17	17
76.0	6.234735	6	6
77.0	6.234736	5	5
78.0	6.234738	11	11
79.0	6.234739	10	10
80.0	6.23474	10	10
81.0	6.234741	11	11
82.0	6.234742	10	10
83.0	6.234742	5	5
84.0	6.234743	5	5
85.0	6.234743	7	7
86.0	6.234743	9	9
87.0	6.234744	4	4
88.0	6.234744	6	6
89.0	6.234744	2	2
90.0	6.234744	2	2
91.0	6.234744	4	4
92.0	6.234745	4	4
93.0	6.234745	8	8
94.0	6.234745	4	4
95.0	6.234745	6	6
96.0	6.234745	3	3
97.0	6.234745	0	0
98.0	6.234745	6	6
99.0	6.234745	4	4
100.0	6.234745	3	3
101.0	0	6	6
102.0	0	5	5
103.0	0	3	3
104.0	0	4	4
105.0	0	5	5
106.0	0	4	4
107.0	0	6	6
108.0	0	7	7
109.0	0	2	2
110.0	0	4	4
111.0	0	4	4
112.0	0	3	3
113.0	0	3	3
114.0	0	3	3
115.0	0	3	3
116.0	0	4	4
117.0	0	3	3
119.0	0	5	5
120.0	0	2	2
121.0	0	1	1
122.0	0	1	1
123.0	0	2	2
124.0	0	1	1
125.0	0	4	4
126.0	0	4	4
127.0	0	1	1
128.0	0	4	4
129.0	0	2	2
130.0	0	3	3
131.0	0	1	1
132.0	0	5	5
133.0	0	2	2
134.0	0	1	1
135.0	0	2	2
136.0	0	3	3
137.0	0	2	2
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
141.0	0	2	2
142.0	0	1	1
143.0	0	2	2
144.0	0	1	1
145.0	0	2	2
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
149.0	0	5	5
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
155.0	0	2	2
156.0	0	4	4
158.0	0	1	1
161.0	0	1	1
163.0	0	2	2
164.0	0	1	1
167.0	0	2	2
168.0	0	1	1
172.0	0	1	1
174.0	0	1	1
175.0	0	1	1
177.0	0	2	2
178.0	0	1	1
181.0	0	2	2
182.0	0	1	1
183.0	0	3	3
184.0	0	1	1
185.0	0	2	2
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
190.0	0	2	2
191.0	0	1	1
193.0	0	1	1
195.0	0	1	1
196.0	0	3	3
198.0	0	1	1
199.0	0	1	1
200.0	0	4	4
202.0	0	2	2
203.0	0	2	2
205.0	0	1	1
208.0	0	1	1
211.0	0	1	1
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
223.0	0	1	1
228.0	0	1	1
229.0	0	1	1
235.0	0	2	2
238.0	0	1	1
241.0	0	1	1
246.0	0	2	2
247.0	0	1	1
251.0	0	1	1
252.0	0	2	2
253.0	0	1	1
254.0	0	1	1
256.0	0	1	1
258.0	0	2	2
260.0	0	1	1
261.0	0	1	1
263.0	0	1	1
266.0	0	1	1
267.0	0	2	2
273.0	0	1	1
275.0	0	2	2
277.0	0	1	1
280.0	0	1	1
284.0	0	2	2
287.0	0	1	1
289.0	0	1	1
294.0	0	1	1
296.0	0	1	1
297.0	0	1	1
301.0	0	1	1
306.0	0	1	1
310.0	0	1	1
313.0	0	1	1
324.0	0	1	1
340.0	0	2	2
345.0	0	1	1
346.0	0	2	2
358.0	0	1	1
361.0	0	1	1
368.0	0	1	1
394.0	0	1	1
414.0	0	1	1
422.0	0	1	1
436.0	0	1	1
453.0	0	1	1
482.0	0	1	1
508.0	0	1	1
510.0	0	2	2
544.0	0	1	1
547.0	0	1	1
565.0	0	1	1
570.0	0	1	1
585.0	0	1	1
586.0	0	1	1
783.0	0	1	1
795.0	0	1	1
847.0	0	1	1
971.0	0	1	1
1733.0	0	1	1
3291.0	0	1	1