## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-06-19/DE_Bay_Mun_1_2014-06-19.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-06-19/DE_Bay_Mun_1_2014-06-19.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-06-19/DE_Bay_Mun_1_2014-06-19.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 08:07:06 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	5621669	17973958	0	0	1107477	503093	0	0.050846	315057289

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	16820899	16820899
2.0	1.944547	365215	365215
3.0	2.836716	6549	6549
4.0	3.679412	576	576
5.0	4.475377	322	322
6.0	5.227204	255	255
7.0	5.93734	186	186
8.0	6.608097	161	161
9.0	7.241658	132	132
10.0	7.840087	122	122
11.0	8.405331	82	82
12.0	8.93923	88	88
13.0	9.443523	80	80
14.0	9.919852	73	73
15.0	10.369766	52	52
16.0	10.794732	54	54
17.0	11.196132	52	52
18.0	11.575273	52	52
19.0	11.93339	41	41
20.0	12.271648	51	51
21.0	12.591148	35	35
22.0	12.892932	28	28
23.0	13.17798	20	20
24.0	13.447222	29	29
25.0	13.701533	29	29
26.0	13.941743	31	31
27.0	14.168631	23	23
28.0	14.382939	23	23
29.0	14.585362	23	23
30.0	14.77656	31	31
31.0	14.957156	19	19
32.0	15.127737	16	16
33.0	15.288859	22	22
34.0	15.441046	15	15
35.0	15.584794	14	14
36.0	15.720571	18	18
37.0	15.848818	12	12
38.0	15.969954	16	16
39.0	16.084373	14	14
40.0	16.192446	21	21
41.0	16.294527	8	8
42.0	16.390947	22	22
43.0	16.48202	10	10
44.0	16.568043	10	10
45.0	16.649296	9	9
46.0	16.726043	11	11
47.0	16.798534	14	14
48.0	16.867005	11	11
49.0	16.931679	12	12
50.0	16.992767	9	9
51.0	17.050468	5	5
52.0	17.104969	15	15
53.0	17.156447	11	11
54.0	17.205071	12	12
55.0	17.250999	11	11
56.0	17.294379	6	6
57.0	17.335354	7	7
58.0	17.374057	7	7
59.0	17.410614	5	5
60.0	17.445144	11	11
61.0	17.477759	9	9
62.0	17.508565	7	7
63.0	17.537663	5	5
64.0	17.565147	5	5
65.0	17.591107	7	7
66.0	17.615628	10	10
67.0	17.638789	1	1
68.0	17.660666	8	8
69.0	17.681329	5	5
70.0	17.700847	8	8
71.0	17.719282	4	4
72.0	17.736695	3	3
73.0	17.753143	5	5
74.0	17.768678	3	3
75.0	17.783352	2	2
76.0	17.797212	1	1
77.0	17.810304	7	7
78.0	17.822669	4	4
79.0	17.834349	2	2
80.0	17.845381	5	5
81.0	17.855802	3	3
82.0	17.865644	2	2
83.0	17.874941	5	5
84.0	17.883723	5	5
85.0	17.892017	3	3
86.0	17.899851	3	3
87.0	17.907251	5	5
88.0	17.914241	6	6
89.0	17.920843	6	6
90.0	17.927079	5	5
91.0	17.932969	5	5
92.0	17.938532	4	4
93.0	17.943787	4	4
94.0	17.948751	3	3
95.0	17.953439	5	5
96.0	17.957867	6	6
97.0	17.96205	3	3
98.0	17.966001	4	4
99.0	17.969733	4	4
100.0	17.973258	4	4
101.0	0	7	7
102.0	0	2	2
103.0	0	6	6
104.0	0	4	4
105.0	0	1	1
106.0	0	2	2
107.0	0	6	6
108.0	0	2	2
109.0	0	1	1
110.0	0	2	2
112.0	0	3	3
113.0	0	2	2
114.0	0	5	5
115.0	0	2	2
116.0	0	3	3
119.0	0	3	3
120.0	0	5	5
121.0	0	5	5
122.0	0	5	5
123.0	0	5	5
124.0	0	1	1
125.0	0	2	2
126.0	0	3	3
127.0	0	3	3
128.0	0	2	2
129.0	0	1	1
130.0	0	1	1
131.0	0	2	2
132.0	0	1	1
133.0	0	2	2
135.0	0	1	1
136.0	0	1	1
138.0	0	3	3
140.0	0	1	1
141.0	0	1	1
143.0	0	2	2
144.0	0	2	2
145.0	0	5	5
147.0	0	1	1
148.0	0	1	1
149.0	0	3	3
150.0	0	2	2
151.0	0	2	2
153.0	0	1	1
154.0	0	4	4
155.0	0	2	2
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	3	3
160.0	0	3	3
161.0	0	4	4
162.0	0	3	3
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
170.0	0	4	4
171.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	4	4
175.0	0	3	3
177.0	0	1	1
178.0	0	2	2
180.0	0	1	1
181.0	0	3	3
182.0	0	4	4
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
189.0	0	1	1
190.0	0	3	3
191.0	0	3	3
192.0	0	1	1
193.0	0	3	3
194.0	0	1	1
195.0	0	1	1
196.0	0	3	3
197.0	0	1	1
200.0	0	3	3
201.0	0	1	1
202.0	0	1	1
205.0	0	3	3
207.0	0	1	1
208.0	0	2	2
209.0	0	2	2
210.0	0	3	3
211.0	0	1	1
212.0	0	1	1
215.0	0	1	1
217.0	0	1	1
221.0	0	1	1
222.0	0	1	1
225.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	1	1
231.0	0	1	1
233.0	0	1	1
235.0	0	1	1
241.0	0	1	1
243.0	0	1	1
245.0	0	1	1
248.0	0	1	1
250.0	0	1	1
252.0	0	1	1
253.0	0	2	2
256.0	0	1	1
257.0	0	2	2
260.0	0	1	1
263.0	0	2	2
264.0	0	1	1
265.0	0	1	1
268.0	0	1	1
270.0	0	1	1
274.0	0	2	2
278.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	3	3
283.0	0	1	1
286.0	0	2	2
287.0	0	1	1
288.0	0	1	1
290.0	0	1	1
292.0	0	1	1
293.0	0	2	2
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
301.0	0	3	3
302.0	0	1	1
303.0	0	2	2
305.0	0	1	1
307.0	0	1	1
309.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	1	1
319.0	0	3	3
335.0	0	1	1
339.0	0	1	1
341.0	0	3	3
343.0	0	2	2
344.0	0	1	1
349.0	0	1	1
357.0	0	1	1
363.0	0	1	1
365.0	0	1	1
367.0	0	3	3
372.0	0	1	1
378.0	0	3	3
380.0	0	1	1
381.0	0	1	1
385.0	0	1	1
386.0	0	1	1
389.0	0	1	1
391.0	0	1	1
395.0	0	1	1
399.0	0	1	1
403.0	0	1	1
409.0	0	2	2
413.0	0	1	1
438.0	0	1	1
453.0	0	1	1
466.0	0	1	1
467.0	0	1	1
472.0	0	1	1
491.0	0	1	1
525.0	0	1	1
527.0	0	1	1
546.0	0	1	1
566.0	0	1	1
578.0	0	1	1
591.0	0	1	1
607.0	0	1	1
608.0	0	1	1
678.0	0	1	1
702.0	0	1	1
707.0	0	1	1
723.0	0	1	1