## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-07-27/TR_Ank_Yes_1_2016-07-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-07-27/TR_Ank_Yes_1_2016-07-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-07-27/TR_Ank_Yes_1_2016-07-27.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 09:10:16 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	35226650	11980050	0	0	7973737	1008296	0	0.168793	67118338

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9943248	9943248
2.0	1.836531	662006	662006
3.0	2.536316	52513	52513
4.0	3.121707	6557	6557
5.0	3.611405	2109	2109
6.0	4.021053	1181	1181
7.0	4.363737	761	761
8.0	4.650402	574	574
9.0	4.890206	423	423
10.0	5.09081	342	342
11.0	5.258621	270	270
12.0	5.399001	212	212
13.0	5.516433	195	195
14.0	5.614668	143	143
15.0	5.696845	135	135
16.0	5.765589	137	137
17.0	5.823095	127	127
18.0	5.871201	109	109
19.0	5.911442	84	84
20.0	5.945106	113	113
21.0	5.973267	100	100
22.0	5.996824	91	91
23.0	6.01653	88	88
24.0	6.033015	84	84
25.0	6.046806	86	86
26.0	6.058342	82	82
27.0	6.067992	78	78
28.0	6.076064	84	84
29.0	6.082817	76	76
30.0	6.088467	68	68
31.0	6.093192	70	70
32.0	6.097145	54	54
33.0	6.100452	47	47
34.0	6.103219	41	41
35.0	6.105533	49	49
36.0	6.107469	43	43
37.0	6.109088	47	47
38.0	6.110443	42	42
39.0	6.111576	28	28
40.0	6.112524	33	33
41.0	6.113317	40	40
42.0	6.113981	39	39
43.0	6.114536	31	31
44.0	6.115	29	29
45.0	6.115388	27	27
46.0	6.115713	23	23
47.0	6.115985	26	26
48.0	6.116212	25	25
49.0	6.116402	25	25
50.0	6.116561	17	17
51.0	6.116694	20	20
52.0	6.116806	13	13
53.0	6.116899	23	23
54.0	6.116977	14	14
55.0	6.117042	19	19
56.0	6.117096	15	15
57.0	6.117142	9	9
58.0	6.11718	11	11
59.0	6.117212	10	10
60.0	6.117239	15	15
61.0	6.117261	11	11
62.0	6.11728	11	11
63.0	6.117295	9	9
64.0	6.117308	15	15
65.0	6.117319	11	11
66.0	6.117329	9	9
67.0	6.117336	13	13
68.0	6.117343	12	12
69.0	6.117348	9	9
70.0	6.117352	15	15
71.0	6.117356	8	8
72.0	6.117359	9	9
73.0	6.117362	14	14
74.0	6.117364	18	18
75.0	6.117366	9	9
76.0	6.117368	6	6
77.0	6.117369	8	8
78.0	6.11737	15	15
79.0	6.117371	8	8
80.0	6.117372	7	7
81.0	6.117372	6	6
82.0	6.117373	5	5
83.0	6.117373	13	13
84.0	6.117374	15	15
85.0	6.117374	7	7
86.0	6.117374	11	11
87.0	6.117374	10	10
88.0	6.117374	12	12
89.0	6.117375	17	17
90.0	6.117375	14	14
91.0	6.117375	15	15
92.0	6.117375	10	10
93.0	6.117375	7	7
94.0	6.117375	12	12
95.0	6.117375	9	9
96.0	6.117375	11	11
97.0	6.117375	3	3
98.0	6.117375	11	11
99.0	6.117375	11	11
100.0	6.117375	7	7
101.0	0	10	10
102.0	0	5	5
103.0	0	9	9
104.0	0	10	10
105.0	0	10	10
106.0	0	11	11
107.0	0	6	6
108.0	0	4	4
109.0	0	4	4
110.0	0	4	4
111.0	0	6	6
112.0	0	7	7
113.0	0	10	10
114.0	0	3	3
115.0	0	3	3
116.0	0	8	8
117.0	0	5	5
118.0	0	6	6
119.0	0	7	7
120.0	0	9	9
121.0	0	4	4
122.0	0	5	5
123.0	0	5	5
124.0	0	1	1
125.0	0	5	5
126.0	0	7	7
127.0	0	5	5
128.0	0	3	3
129.0	0	5	5
130.0	0	1	1
131.0	0	2	2
132.0	0	4	4
133.0	0	3	3
134.0	0	5	5
135.0	0	4	4
136.0	0	3	3
137.0	0	3	3
138.0	0	5	5
139.0	0	2	2
140.0	0	5	5
141.0	0	6	6
142.0	0	1	1
143.0	0	3	3
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
147.0	0	2	2
148.0	0	4	4
149.0	0	7	7
150.0	0	2	2
151.0	0	6	6
152.0	0	3	3
153.0	0	3	3
154.0	0	2	2
155.0	0	3	3
156.0	0	3	3
157.0	0	2	2
158.0	0	3	3
159.0	0	3	3
160.0	0	1	1
161.0	0	2	2
162.0	0	1	1
163.0	0	3	3
164.0	0	3	3
166.0	0	1	1
169.0	0	1	1
170.0	0	2	2
173.0	0	1	1
176.0	0	3	3
181.0	0	1	1
182.0	0	2	2
183.0	0	3	3
184.0	0	2	2
185.0	0	2	2
188.0	0	3	3
189.0	0	1	1
195.0	0	4	4
196.0	0	3	3
198.0	0	1	1
200.0	0	1	1
202.0	0	1	1
203.0	0	1	1
205.0	0	5	5
206.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
214.0	0	2	2
215.0	0	2	2
217.0	0	1	1
218.0	0	2	2
219.0	0	1	1
220.0	0	2	2
226.0	0	1	1
228.0	0	1	1
230.0	0	2	2
235.0	0	1	1
236.0	0	1	1
237.0	0	2	2
242.0	0	1	1
243.0	0	2	2
244.0	0	1	1
245.0	0	1	1
252.0	0	2	2
253.0	0	2	2
254.0	0	1	1
259.0	0	1	1
261.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
272.0	0	1	1
273.0	0	1	1
274.0	0	1	1
277.0	0	1	1
281.0	0	1	1
285.0	0	1	1
286.0	0	1	1
289.0	0	1	1
294.0	0	2	2
300.0	0	1	1
302.0	0	1	1
303.0	0	1	1
307.0	0	1	1
314.0	0	1	1
320.0	0	1	1
321.0	0	1	1
335.0	0	1	1
337.0	0	1	1
339.0	0	1	1
341.0	0	2	2
353.0	0	1	1
354.0	0	1	1
362.0	0	1	1
379.0	0	1	1
384.0	0	1	1
389.0	0	1	1
401.0	0	2	2
402.0	0	1	1
414.0	0	1	1
425.0	0	1	1
431.0	0	1	1
438.0	0	1	1
440.0	0	1	1
453.0	0	1	1
457.0	0	1	1
472.0	0	1	1
476.0	0	1	1
482.0	0	1	1
487.0	0	1	1
491.0	0	1	1
501.0	0	1	1
504.0	0	1	1
505.0	0	1	1
512.0	0	1	1
547.0	0	1	1
554.0	0	1	1
569.0	0	1	1
585.0	0	1	1
628.0	0	1	1
816.0	0	1	1
846.0	0	1	1
889.0	0	1	1
955.0	0	1	1
969.0	0	1	1
1145.0	0	1	1
1189.0	0	1	1
1270.0	0	1	1
1554.0	0	1	1