## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-09-01/DK_Mid_Kar_1_2014-09-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-09-01/DK_Mid_Kar_1_2014-09-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DK_Mid_Kar_1_2014-09-01/DK_Mid_Kar_1_2014-09-01.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 08:24:46 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	10453564	16498371	0	0	2153803	538554	0	0.074359	247180353

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15282187	15282187
2.0	1.935433	366427	366427
3.0	2.810466	7579	7579
4.0	3.629002	731	731
5.0	4.394686	371	371
6.0	5.110932	296	296
7.0	5.780932	193	193
8.0	6.407672	163	163
9.0	6.993944	159	159
10.0	7.542363	119	119
11.0	8.055371	96	96
12.0	8.535256	113	113
13.0	8.984156	99	99
14.0	9.404072	85	85
15.0	9.796874	85	85
16.0	10.164315	70	70
17.0	10.50803	50	50
18.0	10.829553	56	56
19.0	11.130316	53	53
20.0	11.411659	58	58
21.0	11.674837	43	43
22.0	11.921022	48	48
23.0	12.151311	52	52
24.0	12.366732	50	50
25.0	12.568243	38	38
26.0	12.756743	34	34
27.0	12.933072	25	25
28.0	13.098016	31	31
29.0	13.25231	30	30
30.0	13.396641	23	23
31.0	13.531653	27	27
32.0	13.657948	38	38
33.0	13.776089	24	24
34.0	13.886601	26	26
35.0	13.989978	19	19
36.0	14.08668	16	16
37.0	14.177139	23	23
38.0	14.261756	25	25
39.0	14.34091	17	17
40.0	14.414954	10	10
41.0	14.484216	19	19
42.0	14.549007	16	16
43.0	14.609614	15	15
44.0	14.666307	18	18
45.0	14.719341	16	16
46.0	14.76895	18	18
47.0	14.815355	14	14
48.0	14.858765	10	10
49.0	14.899372	14	14
50.0	14.937357	14	14
51.0	14.972889	10	10
52.0	15.006127	11	11
53.0	15.037219	13	13
54.0	15.066303	12	12
55.0	15.09351	14	14
56.0	15.11896	11	11
57.0	15.142766	13	13
58.0	15.165036	15	15
59.0	15.185867	12	12
60.0	15.205354	7	7
61.0	15.223582	5	5
62.0	15.240633	6	6
63.0	15.256584	8	8
64.0	15.271504	7	7
65.0	15.285462	8	8
66.0	15.298518	11	11
67.0	15.310731	7	7
68.0	15.322155	7	7
69.0	15.332842	6	6
70.0	15.342839	6	6
71.0	15.35219	10	10
72.0	15.360937	8	8
73.0	15.36912	7	7
74.0	15.376774	7	7
75.0	15.383935	11	11
76.0	15.390632	10	10
77.0	15.396898	6	6
78.0	15.402759	9	9
79.0	15.408241	7	7
80.0	15.413369	6	6
81.0	15.418167	3	3
82.0	15.422654	5	5
83.0	15.426852	5	5
84.0	15.430779	5	5
85.0	15.434452	8	8
86.0	15.437888	2	2
87.0	15.441102	7	7
88.0	15.444109	3	3
89.0	15.446921	4	4
90.0	15.449552	6	6
91.0	15.452013	5	5
92.0	15.454316	3	3
93.0	15.456469	7	7
94.0	15.458484	13	13
95.0	15.460368	5	5
96.0	15.462131	6	6
97.0	15.46378	5	5
98.0	15.465322	2	2
99.0	15.466765	2	2
100.0	15.468115	3	3
101.0	0	1	1
102.0	0	5	5
103.0	0	6	6
104.0	0	3	3
105.0	0	4	4
106.0	0	5	5
107.0	0	3	3
108.0	0	7	7
109.0	0	2	2
110.0	0	5	5
111.0	0	3	3
112.0	0	4	4
113.0	0	2	2
114.0	0	3	3
115.0	0	3	3
117.0	0	4	4
118.0	0	7	7
119.0	0	2	2
121.0	0	1	1
122.0	0	7	7
124.0	0	3	3
126.0	0	2	2
127.0	0	4	4
128.0	0	3	3
129.0	0	8	8
130.0	0	2	2
131.0	0	6	6
132.0	0	1	1
133.0	0	3	3
134.0	0	5	5
135.0	0	1	1
136.0	0	4	4
137.0	0	3	3
138.0	0	3	3
139.0	0	2	2
140.0	0	1	1
141.0	0	2	2
142.0	0	5	5
143.0	0	2	2
144.0	0	2	2
145.0	0	3	3
146.0	0	4	4
147.0	0	2	2
148.0	0	3	3
149.0	0	5	5
150.0	0	1	1
151.0	0	2	2
152.0	0	2	2
153.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
162.0	0	1	1
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
166.0	0	1	1
167.0	0	3	3
169.0	0	1	1
170.0	0	2	2
171.0	0	1	1
173.0	0	2	2
175.0	0	1	1
176.0	0	1	1
177.0	0	3	3
178.0	0	2	2
179.0	0	1	1
180.0	0	2	2
181.0	0	3	3
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	3	3
186.0	0	4	4
187.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
197.0	0	1	1
199.0	0	1	1
201.0	0	2	2
202.0	0	2	2
203.0	0	4	4
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
210.0	0	2	2
211.0	0	1	1
215.0	0	1	1
220.0	0	1	1
224.0	0	1	1
225.0	0	3	3
226.0	0	2	2
227.0	0	2	2
228.0	0	1	1
229.0	0	2	2
230.0	0	1	1
231.0	0	2	2
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
240.0	0	1	1
241.0	0	3	3
243.0	0	2	2
244.0	0	1	1
246.0	0	1	1
250.0	0	3	3
252.0	0	1	1
255.0	0	1	1
256.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	1	1
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	2	2
278.0	0	2	2
281.0	0	1	1
282.0	0	2	2
284.0	0	2	2
285.0	0	3	3
286.0	0	1	1
289.0	0	1	1
290.0	0	1	1
293.0	0	1	1
294.0	0	1	1
295.0	0	1	1
302.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
308.0	0	1	1
313.0	0	1	1
316.0	0	2	2
317.0	0	1	1
322.0	0	1	1
323.0	0	2	2
330.0	0	1	1
333.0	0	3	3
335.0	0	3	3
336.0	0	1	1
337.0	0	2	2
339.0	0	1	1
346.0	0	1	1
350.0	0	1	1
357.0	0	1	1
359.0	0	1	1
361.0	0	1	1
367.0	0	1	1
369.0	0	1	1
371.0	0	1	1
375.0	0	1	1
376.0	0	1	1
383.0	0	1	1
388.0	0	1	1
389.0	0	1	1
394.0	0	1	1
397.0	0	1	1
399.0	0	1	1
402.0	0	1	1
404.0	0	1	1
405.0	0	1	1
410.0	0	1	1
416.0	0	1	1
417.0	0	1	1
427.0	0	1	1
429.0	0	1	1
434.0	0	1	1
447.0	0	1	1
450.0	0	1	1
453.0	0	1	1
456.0	0	1	1
460.0	0	1	1
466.0	0	1	1
475.0	0	1	1
478.0	0	1	1
482.0	0	1	1
491.0	0	1	1
494.0	0	1	1
498.0	0	1	1
513.0	0	1	1
521.0	0	1	1
531.0	0	1	1
536.0	0	1	1
539.0	0	1	1
549.0	0	1	1
555.0	0	1	1
572.0	0	1	1
576.0	0	1	1
581.0	0	1	1
583.0	0	1	1
590.0	0	1	1
605.0	0	1	1
637.0	0	1	1
665.0	0	1	1
684.0	0	1	1
741.0	0	1	1
762.0	0	1	1
770.0	0	1	1
834.0	0	1	1
954.0	0	1	1
1010.0	0	1	1