## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-09-27/TR_Ank_Yes_1_2016-09-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-09-27/TR_Ank_Yes_1_2016-09-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2016-09-27/TR_Ank_Yes_1_2016-09-27.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 09:09:14 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	35773193	11543822	0	0	9018272	975267	0	0.186352	64414953

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9577398	9577398
2.0	1.83593	621966	621966
3.0	2.534709	49079	49079
4.0	3.11884	6136	6136
5.0	3.607132	2070	2070
6.0	4.01531	1195	1195
7.0	4.356519	814	814
8.0	4.641745	606	606
9.0	4.880174	440	440
10.0	5.079485	357	357
11.0	5.246094	273	273
12.0	5.385368	235	235
13.0	5.501791	195	195
14.0	5.599113	165	165
15.0	5.680467	156	156
16.0	5.748473	162	162
17.0	5.805322	127	127
18.0	5.852843	107	107
19.0	5.892568	112	112
20.0	5.925775	114	114
21.0	5.953534	85	85
22.0	5.976738	99	99
23.0	5.996135	97	97
24.0	6.01235	101	101
25.0	6.025904	68	68
26.0	6.037235	79	79
27.0	6.046706	72	72
28.0	6.054624	74	74
29.0	6.061242	74	74
30.0	6.066775	63	63
31.0	6.0714	67	67
32.0	6.075266	63	63
33.0	6.078497	45	45
34.0	6.081199	57	57
35.0	6.083457	44	44
36.0	6.085345	41	41
37.0	6.086923	53	53
38.0	6.088242	45	45
39.0	6.089345	44	44
40.0	6.090267	42	42
41.0	6.091037	43	43
42.0	6.091681	31	31
43.0	6.09222	34	34
44.0	6.09267	34	34
45.0	6.093046	31	31
46.0	6.093361	25	25
47.0	6.093624	32	32
48.0	6.093843	18	18
49.0	6.094027	19	19
50.0	6.094181	29	29
51.0	6.094309	25	25
52.0	6.094416	25	25
53.0	6.094506	28	28
54.0	6.094581	21	21
55.0	6.094644	13	13
56.0	6.094696	9	9
57.0	6.09474	15	15
58.0	6.094777	14	14
59.0	6.094807	19	19
60.0	6.094833	17	17
61.0	6.094854	16	16
62.0	6.094872	13	13
63.0	6.094887	10	10
64.0	6.094899	10	10
65.0	6.09491	8	8
66.0	6.094919	18	18
67.0	6.094926	9	9
68.0	6.094932	6	6
69.0	6.094937	6	6
70.0	6.094941	8	8
71.0	6.094945	8	8
72.0	6.094948	12	12
73.0	6.09495	11	11
74.0	6.094953	10	10
75.0	6.094954	13	13
76.0	6.094956	12	12
77.0	6.094957	9	9
78.0	6.094958	12	12
79.0	6.094959	5	5
80.0	6.09496	8	8
81.0	6.09496	13	13
82.0	6.094961	9	9
83.0	6.094961	10	10
84.0	6.094961	13	13
85.0	6.094962	11	11
86.0	6.094962	8	8
87.0	6.094962	16	16
88.0	6.094962	7	7
89.0	6.094962	11	11
90.0	6.094963	12	12
91.0	6.094963	8	8
92.0	6.094963	13	13
93.0	6.094963	11	11
94.0	6.094963	6	6
95.0	6.094963	5	5
96.0	6.094963	16	16
97.0	6.094963	12	12
98.0	6.094963	5	5
99.0	6.094963	5	5
100.0	6.094963	3	3
101.0	0	10	10
102.0	0	9	9
103.0	0	5	5
104.0	0	4	4
105.0	0	6	6
106.0	0	6	6
107.0	0	6	6
108.0	0	9	9
109.0	0	6	6
110.0	0	10	10
111.0	0	4	4
112.0	0	4	4
113.0	0	9	9
114.0	0	4	4
115.0	0	6	6
116.0	0	6	6
117.0	0	6	6
118.0	0	5	5
119.0	0	4	4
120.0	0	4	4
121.0	0	4	4
122.0	0	4	4
123.0	0	6	6
124.0	0	4	4
125.0	0	7	7
126.0	0	4	4
127.0	0	3	3
128.0	0	6	6
129.0	0	4	4
130.0	0	7	7
131.0	0	6	6
132.0	0	2	2
133.0	0	6	6
134.0	0	3	3
135.0	0	2	2
136.0	0	3	3
137.0	0	8	8
138.0	0	6	6
139.0	0	4	4
140.0	0	2	2
141.0	0	1	1
143.0	0	1	1
144.0	0	4	4
145.0	0	7	7
146.0	0	1	1
147.0	0	3	3
148.0	0	4	4
149.0	0	2	2
150.0	0	4	4
151.0	0	1	1
152.0	0	5	5
153.0	0	3	3
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
158.0	0	3	3
159.0	0	4	4
160.0	0	2	2
161.0	0	2	2
162.0	0	2	2
163.0	0	1	1
164.0	0	2	2
165.0	0	3	3
169.0	0	1	1
171.0	0	2	2
172.0	0	6	6
173.0	0	1	1
174.0	0	3	3
175.0	0	1	1
176.0	0	1	1
177.0	0	3	3
178.0	0	4	4
179.0	0	2	2
181.0	0	1	1
184.0	0	1	1
185.0	0	5	5
186.0	0	3	3
187.0	0	2	2
188.0	0	1	1
192.0	0	1	1
193.0	0	3	3
194.0	0	2	2
195.0	0	2	2
197.0	0	2	2
198.0	0	1	1
199.0	0	2	2
200.0	0	1	1
203.0	0	2	2
204.0	0	3	3
205.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
216.0	0	3	3
217.0	0	1	1
218.0	0	1	1
219.0	0	2	2
221.0	0	2	2
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	2	2
229.0	0	3	3
230.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
237.0	0	1	1
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
243.0	0	1	1
244.0	0	1	1
247.0	0	1	1
251.0	0	1	1
252.0	0	1	1
255.0	0	1	1
256.0	0	1	1
259.0	0	1	1
262.0	0	1	1
263.0	0	2	2
266.0	0	1	1
267.0	0	1	1
271.0	0	2	2
280.0	0	1	1
290.0	0	1	1
297.0	0	2	2
300.0	0	1	1
302.0	0	2	2
303.0	0	1	1
305.0	0	1	1
310.0	0	2	2
312.0	0	2	2
316.0	0	1	1
317.0	0	1	1
323.0	0	1	1
324.0	0	1	1
327.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
348.0	0	1	1
350.0	0	1	1
354.0	0	1	1
360.0	0	1	1
361.0	0	1	1
362.0	0	1	1
365.0	0	1	1
377.0	0	1	1
379.0	0	2	2
387.0	0	2	2
392.0	0	1	1
394.0	0	1	1
399.0	0	1	1
406.0	0	1	1
414.0	0	1	1
423.0	0	1	1
426.0	0	2	2
432.0	0	1	1
437.0	0	1	1
439.0	0	1	1
443.0	0	1	1
444.0	0	1	1
450.0	0	1	1
453.0	0	1	1
462.0	0	1	1
472.0	0	1	1
483.0	0	1	1
490.0	0	1	1
492.0	0	1	1
506.0	0	1	1
523.0	0	1	1
526.0	0	1	1
541.0	0	1	1
543.0	0	1	1
595.0	0	1	1
599.0	0	1	1
616.0	0	1	1
630.0	0	1	1
640.0	0	1	1
719.0	0	1	1
801.0	0	1	1
807.0	0	1	1
1048.0	0	1	1
1105.0	0	1	1
1129.0	0	1	1
1189.0	0	1	1
1646.0	0	1	1
3206.0	0	1	1