## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Mun_5_Sep_2020/DE_Mun_5_Sep_2020.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Mun_5_Sep_2020/DE_Mun_5_Sep_2020.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/DE_Mun_5_Sep_2020/DE_Mun_5_Sep_2020.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 03:48:16 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	3648083	21928910	0	0	1939461	3982032	166715	0.208469	54576205

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006225	14495455	0	14607217
2.0	1.679503	2593086	164062	2522095
3.0	2.130001	457805	1241	427779
4.0	2.431435	79173	17	70854
5.0	2.633128	13987	2	12103
6.0	2.768083	2770	2	2343
7.0	2.858383	738	0	646
8.0	2.918804	342	0	332
9.0	2.959233	201	0	193
10.0	2.986284	170	0	175
11.0	3.004384	103	0	97
12.0	3.016495	86	0	86
13.0	3.024599	80	0	79
14.0	3.030021	50	0	50
15.0	3.033649	58	0	56
16.0	3.036077	54	1	57
17.0	3.037701	49	0	46
18.0	3.038788	36	0	35
19.0	3.039515	26	0	27
20.0	3.040002	23	0	23
21.0	3.040328	35	0	36
22.0	3.040545	24	0	23
23.0	3.040691	29	0	32
24.0	3.040789	28	0	28
25.0	3.040854	21	0	21
26.0	3.040898	18	0	14
27.0	3.040927	21	0	22
28.0	3.040946	13	0	14
29.0	3.04096	16	1	15
30.0	3.040968	14	0	14
31.0	3.040974	13	0	14
32.0	3.040978	11	0	9
33.0	3.040981	14	0	15
34.0	3.040982	10	0	9
35.0	3.040984	9	0	9
36.0	3.040984	8	0	9
37.0	3.040985	9	0	8
38.0	3.040985	9	0	9
39.0	3.040986	6	0	6
40.0	3.040986	10	0	10
41.0	3.040986	3	0	3
42.0	3.040986	7	0	7
43.0	3.040986	2	0	4
44.0	3.040986	14	0	12
45.0	3.040986	6	0	6
46.0	3.040986	7	0	7
47.0	3.040986	5	0	5
48.0	3.040986	11	0	11
49.0	3.040986	8	0	8
50.0	3.040986	7	0	7
51.0	3.040986	11	0	11
52.0	3.040986	7	0	8
53.0	3.040986	9	0	9
54.0	3.040986	9	0	9
55.0	3.040986	7	0	7
56.0	3.040986	10	0	9
57.0	3.040986	6	0	7
58.0	3.040986	4	0	5
59.0	3.040986	8	0	9
60.0	3.040986	5	1	3
61.0	3.040986	3	0	4
62.0	3.040986	10	0	9
63.0	3.040986	3	0	2
64.0	3.040986	2	0	2
65.0	3.040986	6	0	7
66.0	3.040986	4	0	4
67.0	3.040986	3	0	3
68.0	3.040986	3	0	5
69.0	3.040986	6	0	4
70.0	3.040986	4	0	3
71.0	3.040986	3	0	3
72.0	3.040986	2	0	2
73.0	3.040986	5	0	5
74.0	3.040986	3	0	3
75.0	3.040986	1	0	2
76.0	3.040986	3	0	3
77.0	3.040986	2	0	2
78.0	3.040986	3	0	2
79.0	3.040986	4	0	4
80.0	3.040986	3	0	3
81.0	3.040986	6	0	7
82.0	3.040986	2	0	1
83.0	3.040986	4	0	5
84.0	3.040986	5	0	4
85.0	3.040986	0	0	0
86.0	3.040986	2	0	2
87.0	3.040986	1	0	1
88.0	3.040986	1	0	1
89.0	3.040986	1	0	1
90.0	3.040986	2	0	2
91.0	3.040986	0	0	0
92.0	3.040986	0	0	0
93.0	3.040986	2	0	3
94.0	3.040986	3	0	3
95.0	3.040986	2	0	1
96.0	3.040986	1	0	1
97.0	3.040986	3	0	3
98.0	3.040986	0	0	1
99.0	3.040986	5	0	4
100.0	3.040986	3	0	3
101.0	0	5	0	5
102.0	0	2	0	3
103.0	0	1	0	0
104.0	0	2	0	2
105.0	0	6	0	6
106.0	0	1	0	1
107.0	0	1	0	1
109.0	0	3	0	3
110.0	0	4	0	4
111.0	0	2	0	2
112.0	0	2	0	3
113.0	0	2	0	1
114.0	0	2	0	2
115.0	0	1	0	1
116.0	0	4	0	4
117.0	0	1	0	2
118.0	0	1	0	0
119.0	0	4	0	4
121.0	0	0	0	1
122.0	0	1	0	0
123.0	0	2	0	2
124.0	0	2	0	2
125.0	0	1	0	1
126.0	0	2	0	2
128.0	0	1	0	1
130.0	0	1	0	1
131.0	0	2	0	3
132.0	0	1	0	1
133.0	0	2	0	1
134.0	0	2	0	3
135.0	0	1	0	0
139.0	0	1	0	1
140.0	0	2	0	2
141.0	0	0	0	1
142.0	0	1	0	0
143.0	0	1	0	2
144.0	0	2	0	1
145.0	0	0	0	1
147.0	0	3	0	2
149.0	0	1	0	1
150.0	0	2	0	2
151.0	0	4	0	4
152.0	0	1	0	1
154.0	0	1	0	1
155.0	0	1	0	1
157.0	0	1	0	1
158.0	0	1	0	1
160.0	0	0	0	1
161.0	0	1	0	0
167.0	0	1	0	1
169.0	0	2	0	2
170.0	0	3	0	3
171.0	0	1	0	2
172.0	0	2	0	2
173.0	0	2	0	1
174.0	0	1	0	2
175.0	0	1	0	0
176.0	0	0	0	1
177.0	0	1	0	0
179.0	0	1	0	1
180.0	0	1	0	1
181.0	0	0	0	1
182.0	0	2	0	1
183.0	0	1	0	1
185.0	0	1	0	1
186.0	0	1	0	2
187.0	0	1	0	1
188.0	0	2	0	1
189.0	0	0	0	1
191.0	0	3	0	3
192.0	0	2	0	2
193.0	0	1	0	1
194.0	0	1	0	0
196.0	0	1	0	1
199.0	0	1	0	1
206.0	0	1	0	2
207.0	0	1	0	0
211.0	0	1	0	1
212.0	0	2	0	2
213.0	0	1	0	1
214.0	0	1	0	1
216.0	0	1	0	1
218.0	0	1	0	1
220.0	0	1	0	1
223.0	0	1	0	1
224.0	0	3	0	3
225.0	0	1	0	1
227.0	0	1	0	1
230.0	0	1	0	2
231.0	0	1	0	1
232.0	0	2	0	1
233.0	0	1	0	1
240.0	0	1	0	1
242.0	0	1	0	1
244.0	0	2	0	2
245.0	0	0	0	1
246.0	0	0	0	1
247.0	0	3	0	1
250.0	0	1	0	1
251.0	0	1	0	1
256.0	0	1	0	2
258.0	0	1	0	0
259.0	0	0	0	1
261.0	0	1	0	0
262.0	0	0	0	1
264.0	0	2	0	1
265.0	0	1	0	1
266.0	0	1	0	1
267.0	0	2	0	2
269.0	0	1	0	1
274.0	0	1	0	1
282.0	0	1	0	1
284.0	0	1	0	1
302.0	0	0	0	1
304.0	0	1	0	0
306.0	0	1	0	1
308.0	0	1	0	1
310.0	0	1	0	1
312.0	0	0	0	1
313.0	0	1	0	0
321.0	0	2	0	2
331.0	0	0	0	1
333.0	0	1	0	0
343.0	0	0	0	1
344.0	0	1	0	0
345.0	0	1	0	1
352.0	0	1	0	1
353.0	0	0	0	1
354.0	0	1	0	0
356.0	0	0	0	1
359.0	0	1	0	0
365.0	0	1	0	1
370.0	0	0	0	1
371.0	0	1	0	0
374.0	0	1	0	1
375.0	0	0	0	1
378.0	0	1	0	0
384.0	0	0	0	1
385.0	0	1	0	0
388.0	0	0	0	1
389.0	0	2	0	1
405.0	0	0	0	1
406.0	0	1	0	1
408.0	0	2	0	1
422.0	0	0	0	1
423.0	0	1	0	0
425.0	0	1	0	1
426.0	0	0	0	1
428.0	0	1	0	0
435.0	0	1	0	1
441.0	0	1	0	1
456.0	0	0	0	1
457.0	0	1	0	0
460.0	0	0	0	1
463.0	0	1	0	0
471.0	0	1	0	1
474.0	0	1	0	1
482.0	0	0	0	1
483.0	0	1	0	0
487.0	0	0	0	1
488.0	0	1	0	0
491.0	0	1	0	2
492.0	0	1	0	0
500.0	0	0	0	1
502.0	0	2	0	1
512.0	0	0	0	1
515.0	0	1	0	0
531.0	0	0	0	1
532.0	0	1	0	0
533.0	0	1	0	1
534.0	0	0	0	1
535.0	0	0	0	1
536.0	0	2	0	0
543.0	0	0	0	1
544.0	0	1	0	0
553.0	0	0	0	1
556.0	0	1	0	0
594.0	0	0	0	1
595.0	0	1	0	0
601.0	0	0	0	1
603.0	0	1	0	0
626.0	0	0	0	1
631.0	0	1	0	0
648.0	0	0	0	1
650.0	0	2	0	1
701.0	0	0	0	1
702.0	0	1	0	0
730.0	0	1	0	2
731.0	0	1	0	0
797.0	0	1	0	1
865.0	0	0	0	1
868.0	0	1	0	0
908.0	0	0	0	1
909.0	0	1	0	0
977.0	0	0	0	1
978.0	0	1	0	0
1018.0	0	0	0	1
1019.0	0	1	0	0
1043.0	0	0	0	1
1045.0	0	1	0	0
1075.0	0	0	0	1
1078.0	0	1	0	0
1134.0	0	1	0	1
1168.0	0	0	0	1
1171.0	0	1	0	0
1228.0	0	0	0	1
1231.0	0	1	0	0
1254.0	0	0	0	1
1258.0	0	1	0	0
1287.0	0	0	0	1
1289.0	0	1	0	0
1351.0	0	1	0	1
1454.0	0	0	0	1
1455.0	0	1	0	1
1458.0	0	1	0	0
1465.0	0	1	0	1
1563.0	0	0	0	1
1564.0	0	1	0	0
2585.0	0	1	0	1
2810.0	0	0	0	1
2811.0	0	1	0	0
6152.0	0	0	0	1
6167.0	0	1	0	0
6392.0	0	0	0	1
6397.0	0	1	0	0
10505.0	0	0	0	1
10533.0	0	1	0	0
24526.0	0	0	0	1
24585.0	0	1	0	0