## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Bro_22_Jul_2021/DE_Bro_22_Jul_2021.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Bro_22_Jul_2021/DE_Bro_22_Jul_2021.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Bro_22_Jul_2021/DE_Bro_22_Jul_2021.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: Wed Dec 21 03:56:13 UTC 2022

## 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	2791675	22272732	0	0	1464276	5446563	231651	0.261051	38898547

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007789	12457214	0	12590533
2.0	1.576248	3028647	226192	2960035
3.0	1.896895	723218	2509	681495
4.0	2.077762	170034	24	154039
5.0	2.179782	40158	7	35284
6.0	2.237328	9875	4	8355
7.0	2.269788	2594	5	2190
8.0	2.288098	858	3	725
9.0	2.298425	410	5	376
10.0	2.304251	257	3	246
11.0	2.307537	199	1	198
12.0	2.30939	148	0	147
13.0	2.310436	134	2	130
14.0	2.311026	101	0	98
15.0	2.311358	99	0	102
16.0	2.311546	75	1	75
17.0	2.311652	75	0	72
18.0	2.311711	55	0	52
19.0	2.311745	48	0	48
20.0	2.311764	41	0	43
21.0	2.311775	44	0	45
22.0	2.311781	36	0	34
23.0	2.311784	32	0	35
24.0	2.311786	36	0	36
25.0	2.311787	28	0	26
26.0	2.311788	22	0	20
27.0	2.311788	28	0	27
28.0	2.311788	15	0	17
29.0	2.311789	25	0	27
30.0	2.311789	26	0	24
31.0	2.311789	18	0	20
32.0	2.311789	26	0	27
33.0	2.311789	27	0	24
34.0	2.311789	12	0	11
35.0	2.311789	8	0	9
36.0	2.311789	18	0	17
37.0	2.311789	13	0	12
38.0	2.311789	8	0	10
39.0	2.311789	10	0	10
40.0	2.311789	10	0	9
41.0	2.311789	11	0	13
42.0	2.311789	16	0	15
43.0	2.311789	9	0	7
44.0	2.311789	11	0	13
45.0	2.311789	12	0	11
46.0	2.311789	11	0	12
47.0	2.311789	7	1	6
48.0	2.311789	3	0	2
49.0	2.311789	7	0	8
50.0	2.311789	7	0	6
51.0	2.311789	8	0	10
52.0	2.311789	8	0	7
53.0	2.311789	6	0	8
54.0	2.311789	9	0	9
55.0	2.311789	5	0	7
56.0	2.311789	10	0	8
57.0	2.311789	5	0	4
58.0	2.311789	4	0	3
59.0	2.311789	10	0	10
60.0	2.311789	7	0	6
61.0	2.311789	4	0	7
62.0	2.311789	8	0	5
63.0	2.311789	2	0	3
64.0	2.311789	5	0	6
65.0	2.311789	7	0	6
66.0	2.311789	4	0	4
67.0	2.311789	1	0	2
68.0	2.311789	5	0	4
69.0	2.311789	8	0	8
70.0	2.311789	4	0	4
71.0	2.311789	4	0	3
72.0	2.311789	7	0	8
73.0	2.311789	4	0	3
74.0	2.311789	3	0	4
75.0	2.311789	2	0	2
76.0	2.311789	2	0	2
77.0	2.311789	4	0	4
78.0	2.311789	4	0	4
79.0	2.311789	1	0	1
80.0	2.311789	4	0	3
81.0	2.311789	3	0	4
82.0	2.311789	7	0	8
83.0	2.311789	5	0	4
84.0	2.311789	3	0	4
85.0	2.311789	5	0	4
86.0	2.311789	2	0	1
87.0	2.311789	6	0	7
88.0	2.311789	3	0	3
89.0	2.311789	8	0	7
90.0	2.311789	2	0	2
91.0	2.311789	5	0	5
92.0	2.311789	0	0	0
93.0	2.311789	2	0	3
94.0	2.311789	2	0	1
95.0	2.311789	3	0	4
96.0	2.311789	7	0	7
97.0	2.311789	4	0	4
98.0	2.311789	4	0	3
99.0	2.311789	1	0	1
100.0	2.311789	2	0	2
101.0	0	1	0	2
102.0	0	2	0	1
103.0	0	1	0	1
104.0	0	1	0	1
105.0	0	4	0	4
106.0	0	1	0	2
107.0	0	2	0	1
108.0	0	2	0	2
109.0	0	0	1	0
110.0	0	1	0	1
111.0	0	2	0	2
113.0	0	1	0	1
115.0	0	6	0	6
116.0	0	2	0	3
117.0	0	1	0	2
118.0	0	3	0	3
119.0	0	5	0	4
121.0	0	1	0	1
122.0	0	3	0	2
123.0	0	2	0	2
125.0	0	2	0	2
126.0	0	3	0	3
127.0	0	1	0	1
128.0	0	2	0	2
129.0	0	1	0	1
130.0	0	2	0	2
131.0	0	3	0	5
132.0	0	2	0	1
133.0	0	2	0	1
134.0	0	1	0	2
135.0	0	3	0	2
136.0	0	1	0	1
137.0	0	1	0	1
138.0	0	0	0	1
139.0	0	1	0	1
140.0	0	2	0	1
141.0	0	2	0	2
142.0	0	1	0	1
143.0	0	1	0	2
144.0	0	4	0	3
145.0	0	3	0	3
148.0	0	1	0	1
150.0	0	2	0	3
151.0	0	2	0	2
152.0	0	2	0	1
153.0	0	0	0	1
154.0	0	1	0	1
155.0	0	1	0	0
156.0	0	1	0	1
158.0	0	2	0	3
159.0	0	2	0	2
160.0	0	1	0	2
161.0	0	5	0	4
162.0	0	2	0	1
163.0	0	1	0	1
165.0	0	2	0	2
168.0	0	1	0	1
169.0	0	1	0	1
171.0	0	1	0	1
172.0	0	1	0	1
173.0	0	1	0	2
174.0	0	4	0	3
175.0	0	1	0	1
176.0	0	1	0	1
177.0	0	2	0	2
178.0	0	1	0	1
181.0	0	1	0	1
183.0	0	1	0	1
184.0	0	2	0	3
185.0	0	1	0	1
186.0	0	2	0	1
187.0	0	1	0	1
189.0	0	1	0	1
190.0	0	1	0	1
191.0	0	1	0	1
192.0	0	2	0	2
194.0	0	1	0	2
195.0	0	2	0	2
196.0	0	3	0	3
197.0	0	2	0	1
199.0	0	1	0	1
203.0	0	1	0	1
205.0	0	2	0	2
207.0	0	2	0	2
208.0	0	1	0	1
210.0	0	1	0	1
211.0	0	0	0	1
212.0	0	4	0	3
215.0	0	1	0	2
217.0	0	1	0	2
218.0	0	4	0	2
219.0	0	1	0	1
221.0	0	0	0	1
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	1	0	0
225.0	0	1	0	1
226.0	0	1	0	1
227.0	0	1	0	2
228.0	0	3	0	2
229.0	0	0	0	1
232.0	0	1	0	0
235.0	0	1	0	1
237.0	0	0	0	1
238.0	0	1	0	1
239.0	0	1	0	0
240.0	0	2	0	2
241.0	0	2	0	2
243.0	0	1	0	1
246.0	0	0	0	1
248.0	0	0	0	1
249.0	0	1	0	1
250.0	0	2	0	0
253.0	0	1	0	2
254.0	0	1	0	0
255.0	0	1	0	1
256.0	0	1	0	1
258.0	0	0	0	1
262.0	0	2	0	1
266.0	0	1	0	1
267.0	0	0	0	1
268.0	0	1	0	0
275.0	0	0	0	2
277.0	0	1	0	1
278.0	0	1	0	0
279.0	0	2	0	2
282.0	0	0	0	1
283.0	0	2	0	0
287.0	0	2	0	2
288.0	0	1	0	1
289.0	0	1	0	1
290.0	0	2	0	2
295.0	0	1	0	1
297.0	0	1	0	1
300.0	0	0	0	1
302.0	0	1	0	1
306.0	0	2	0	1
313.0	0	2	0	2
318.0	0	1	0	2
319.0	0	1	0	0
321.0	0	0	0	2
322.0	0	1	0	0
326.0	0	1	0	0
330.0	0	0	0	1
333.0	0	1	0	0
337.0	0	0	0	1
341.0	0	1	0	0
343.0	0	1	0	1
346.0	0	1	0	1
351.0	0	1	0	2
356.0	0	1	0	0
357.0	0	1	0	2
358.0	0	1	0	0
366.0	0	0	0	1
367.0	0	1	0	1
368.0	0	1	0	0
371.0	0	1	0	1
373.0	0	1	0	1
377.0	0	0	0	1
378.0	0	1	0	0
380.0	0	0	0	1
382.0	0	1	0	0
386.0	0	1	0	1
391.0	0	0	0	1
395.0	0	3	0	2
400.0	0	1	0	1
408.0	0	1	0	1
409.0	0	1	0	1
415.0	0	1	0	1
416.0	0	1	0	2
417.0	0	1	0	0
430.0	0	0	0	1
431.0	0	1	0	0
434.0	0	0	0	1
436.0	0	2	0	1
438.0	0	1	0	1
441.0	0	1	0	1
447.0	0	0	0	1
449.0	0	1	0	0
462.0	0	0	0	1
463.0	0	1	0	0
465.0	0	1	0	1
466.0	0	0	0	1
468.0	0	0	0	1
469.0	0	1	0	0
473.0	0	1	0	0
475.0	0	0	0	1
480.0	0	1	0	1
482.0	0	2	0	1
504.0	0	1	0	1
508.0	0	0	0	1
509.0	0	1	0	0
512.0	0	1	0	1
527.0	0	0	0	1
528.0	0	1	0	0
534.0	0	1	0	2
536.0	0	1	0	1
541.0	0	1	0	1
542.0	0	1	0	1
545.0	0	2	0	1
554.0	0	0	0	1
555.0	0	1	0	0
564.0	0	0	0	1
566.0	0	1	0	0
568.0	0	1	0	1
572.0	0	0	0	1
573.0	0	1	0	0
580.0	0	0	0	1
582.0	0	1	0	0
598.0	0	2	0	2
604.0	0	1	0	1
607.0	0	0	0	1
609.0	0	1	0	0
628.0	0	0	0	1
629.0	0	1	0	0
630.0	0	0	0	1
632.0	0	1	0	1
636.0	0	1	0	0
652.0	0	1	0	1
664.0	0	1	0	1
703.0	0	0	0	1
704.0	0	1	0	1
705.0	0	1	0	0
738.0	0	0	0	1
746.0	0	1	0	0
748.0	0	1	0	1
749.0	0	1	0	1
756.0	0	0	0	1
759.0	0	1	0	0
760.0	0	0	0	1
762.0	0	1	0	0
781.0	0	0	0	1
786.0	0	1	0	1
787.0	0	0	0	1
790.0	0	1	0	0
791.0	0	1	0	0
821.0	0	0	0	1
825.0	0	1	0	0
834.0	0	1	0	1
861.0	0	0	0	1
862.0	0	1	0	0
908.0	0	0	0	1
915.0	0	1	0	0
917.0	0	0	0	1
918.0	0	1	0	0
929.0	0	1	0	1
934.0	0	0	0	1
942.0	0	1	0	0
995.0	0	1	0	1
999.0	0	1	0	1
1004.0	0	0	0	1
1009.0	0	1	0	0
1079.0	0	1	0	1
1086.0	0	0	0	1
1091.0	0	0	0	1
1092.0	0	2	0	0
1230.0	0	0	0	1
1242.0	0	1	0	0
1257.0	0	0	0	1
1264.0	0	1	0	0
1431.0	0	0	0	1
1434.0	0	1	0	0
1532.0	0	0	0	1
1538.0	0	1	0	0
1589.0	0	0	0	1
1595.0	0	1	0	0
1688.0	0	0	0	1
1690.0	0	1	0	0
1741.0	0	0	0	1
1749.0	0	1	0	0
1780.0	0	0	0	1
1789.0	0	1	0	0
1824.0	0	1	0	1
1961.0	0	0	0	1
1963.0	0	1	0	0
2002.0	0	0	0	1
2005.0	0	1	0	0
2033.0	0	1	0	1
2143.0	0	0	0	1
2151.0	0	1	0	0
2273.0	0	0	0	1
2279.0	0	1	0	0
2414.0	0	0	0	1
2426.0	0	1	0	0
3237.0	0	0	0	1
3240.0	0	1	0	0
3260.0	0	0	0	1
3263.0	0	1	0	0
8103.0	0	0	0	1
8118.0	0	1	0	0
8907.0	0	0	0	1
8917.0	0	1	0	0
12656.0	0	0	0	1
12702.0	0	1	0	0
29308.0	0	0	0	1
29416.0	0	1	0	0