## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/DK_Kar_1_Oct_2019/DK_Kar_1_Oct_2019.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/DK_Kar_1_Oct_2019/DK_Kar_1_Oct_2019.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/DK_Kar_1_Oct_2019/DK_Kar_1_Oct_2019.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: Thu Dec 22 18:32:09 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	3693516	24869268	0	0	2005331	6099302	258724	0.265832	43273978

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007782	13912210	0	14061422
2.0	1.57504	3441125	252653	3364354
3.0	1.894336	818886	2748	771970
4.0	2.074061	190545	51	172698
5.0	2.175224	44343	5	38909
6.0	2.232166	10605	9	8935
7.0	2.264218	2713	5	2339
8.0	2.282259	885	2	752
9.0	2.292414	400	1	367
10.0	2.29813	239	4	228
11.0	2.301347	189	2	177
12.0	2.303158	136	1	132
13.0	2.304178	131	1	128
14.0	2.304752	96	2	97
15.0	2.305075	72	2	75
16.0	2.305256	76	0	74
17.0	2.305359	57	2	57
18.0	2.305416	63	2	60
19.0	2.305449	40	0	40
20.0	2.305467	49	0	48
21.0	2.305477	32	0	33
22.0	2.305483	30	0	30
23.0	2.305486	27	0	26
24.0	2.305488	23	0	24
25.0	2.305489	32	0	31
26.0	2.30549	17	0	17
27.0	2.30549	25	0	24
28.0	2.30549	27	0	28
29.0	2.30549	18	0	18
30.0	2.30549	12	0	16
31.0	2.30549	20	0	16
32.0	2.30549	21	0	21
33.0	2.30549	18	0	18
34.0	2.30549	18	0	16
35.0	2.30549	13	1	14
36.0	2.30549	14	0	14
37.0	2.30549	13	0	14
38.0	2.30549	21	0	20
39.0	2.30549	7	0	8
40.0	2.30549	14	0	15
41.0	2.30549	10	0	10
42.0	2.30549	16	0	16
43.0	2.30549	10	0	9
44.0	2.30549	8	0	9
45.0	2.30549	9	0	9
46.0	2.30549	12	0	11
47.0	2.30549	8	0	7
48.0	2.30549	7	0	7
49.0	2.30549	10	0	12
50.0	2.30549	14	0	13
51.0	2.30549	9	0	8
52.0	2.30549	2	0	3
53.0	2.30549	7	0	6
54.0	2.30549	9	0	10
55.0	2.30549	7	0	7
56.0	2.30549	5	0	3
57.0	2.30549	8	0	8
58.0	2.30549	5	0	8
59.0	2.30549	7	0	6
60.0	2.30549	6	0	5
61.0	2.30549	5	0	5
62.0	2.30549	6	0	7
63.0	2.30549	6	0	4
64.0	2.30549	4	0	5
65.0	2.30549	7	0	8
66.0	2.30549	8	0	6
67.0	2.30549	8	0	10
68.0	2.30549	8	0	7
69.0	2.30549	5	0	5
70.0	2.30549	6	0	6
71.0	2.30549	4	0	4
72.0	2.30549	3	0	2
73.0	2.30549	1	1	1
74.0	2.30549	4	0	5
75.0	2.30549	2	0	2
76.0	2.30549	4	0	4
77.0	2.30549	3	0	2
78.0	2.30549	3	0	4
79.0	2.30549	4	0	3
80.0	2.30549	3	0	3
81.0	2.30549	4	0	4
82.0	2.30549	5	0	5
83.0	2.30549	2	0	2
84.0	2.30549	4	0	7
85.0	2.30549	4	0	1
86.0	2.30549	3	0	3
87.0	2.30549	2	0	3
88.0	2.30549	2	0	2
89.0	2.30549	5	0	5
90.0	2.30549	4	0	3
91.0	2.30549	3	0	6
92.0	2.30549	3	0	0
93.0	2.30549	3	0	4
94.0	2.30549	5	0	7
95.0	2.30549	0	0	0
96.0	2.30549	4	0	1
97.0	2.30549	3	0	3
98.0	2.30549	2	0	3
99.0	2.30549	4	0	4
100.0	2.30549	4	0	3
101.0	0	0	0	2
102.0	0	4	0	4
103.0	0	3	0	2
104.0	0	2	0	1
105.0	0	1	0	2
106.0	0	2	0	3
107.0	0	4	0	2
108.0	0	2	0	4
109.0	0	3	0	2
110.0	0	5	0	4
111.0	0	2	0	2
112.0	0	2	0	3
113.0	0	4	0	3
114.0	0	1	0	1
115.0	0	0	0	1
116.0	0	3	0	3
117.0	0	1	0	0
118.0	0	1	0	3
119.0	0	1	0	1
120.0	0	1	0	0
121.0	0	3	0	3
122.0	0	2	0	2
123.0	0	4	0	3
124.0	0	1	0	1
125.0	0	1	0	2
126.0	0	1	0	0
128.0	0	2	0	2
129.0	0	3	0	3
130.0	0	2	0	2
131.0	0	1	0	1
132.0	0	1	0	1
133.0	0	1	0	1
135.0	0	2	0	2
136.0	0	1	0	1
137.0	0	1	0	1
139.0	0	1	0	1
142.0	0	2	0	2
144.0	0	1	0	3
145.0	0	3	0	1
146.0	0	1	0	1
148.0	0	1	0	1
149.0	0	1	0	1
150.0	0	1	0	1
151.0	0	1	0	3
152.0	0	1	0	0
153.0	0	1	0	0
155.0	0	0	0	1
156.0	0	1	0	1
157.0	0	1	0	1
159.0	0	3	0	3
160.0	0	2	0	2
161.0	0	1	0	0
163.0	0	1	0	1
164.0	0	0	0	1
165.0	0	1	0	0
167.0	0	1	0	1
169.0	0	1	0	2
170.0	0	1	0	1
171.0	0	1	0	1
172.0	0	1	0	0
173.0	0	3	0	3
174.0	0	0	0	1
175.0	0	2	0	1
176.0	0	1	0	1
177.0	0	1	0	1
178.0	0	5	0	6
179.0	0	2	0	1
180.0	0	1	0	1
181.0	0	1	0	1
182.0	0	1	0	3
183.0	0	2	0	2
184.0	0	1	0	0
186.0	0	2	0	1
188.0	0	1	0	1
189.0	0	1	0	1
190.0	0	1	0	1
192.0	0	1	0	1
195.0	0	1	0	1
198.0	0	0	0	1
199.0	0	1	0	1
200.0	0	0	0	1
201.0	0	2	0	1
202.0	0	1	0	0
205.0	0	2	0	2
206.0	0	1	0	1
210.0	0	1	0	1
213.0	0	1	0	1
215.0	0	2	0	2
217.0	0	1	0	1
221.0	0	1	0	1
226.0	0	1	0	1
229.0	0	0	0	1
230.0	0	2	0	2
233.0	0	1	0	0
235.0	0	0	0	1
236.0	0	2	0	1
241.0	0	2	0	2
242.0	0	1	0	1
243.0	0	0	0	1
244.0	0	0	0	1
245.0	0	3	0	1
246.0	0	0	0	1
247.0	0	1	0	0
251.0	0	1	0	1
253.0	0	1	0	1
258.0	0	0	0	2
260.0	0	2	0	2
261.0	0	1	0	0
262.0	0	1	0	0
263.0	0	1	0	1
264.0	0	0	0	1
265.0	0	2	0	1
268.0	0	0	0	1
269.0	0	1	0	0
271.0	0	0	0	1
272.0	0	1	0	0
279.0	0	1	0	1
280.0	0	0	0	1
281.0	0	1	0	0
283.0	0	0	0	1
285.0	0	1	0	2
286.0	0	1	0	2
287.0	0	2	0	0
288.0	0	1	0	2
290.0	0	1	0	0
291.0	0	1	0	0
292.0	0	0	0	1
294.0	0	0	0	1
297.0	0	2	0	0
298.0	0	1	0	1
300.0	0	2	0	2
301.0	0	1	0	1
305.0	0	1	0	1
309.0	0	1	0	1
311.0	0	0	0	1
312.0	0	1	0	0
316.0	0	1	0	1
320.0	0	1	0	1
322.0	0	0	0	1
325.0	0	1	0	0
327.0	0	1	0	1
328.0	0	0	0	1
329.0	0	0	0	1
330.0	0	2	0	0
334.0	0	1	0	1
337.0	0	1	0	1
342.0	0	1	0	1
345.0	0	1	0	1
347.0	0	0	0	1
351.0	0	0	0	1
352.0	0	1	0	0
353.0	0	1	0	0
355.0	0	1	0	1
357.0	0	0	0	1
358.0	0	2	0	1
360.0	0	0	0	1
362.0	0	1	0	0
398.0	0	1	0	1
408.0	0	1	0	1
411.0	0	0	0	1
413.0	0	1	0	1
414.0	0	1	0	0
415.0	0	1	0	1
423.0	0	0	0	1
424.0	0	1	0	1
425.0	0	1	0	0
429.0	0	1	0	1
438.0	0	0	0	1
439.0	0	1	0	0
443.0	0	1	0	1
452.0	0	0	0	1
456.0	0	1	0	0
460.0	0	1	0	1
462.0	0	1	0	1
478.0	0	1	0	1
480.0	0	0	0	1
482.0	0	2	0	1
490.0	0	1	0	1
491.0	0	0	0	1
492.0	0	1	0	2
493.0	0	1	0	0
495.0	0	1	0	1
501.0	0	1	0	1
504.0	0	1	0	0
513.0	0	0	0	1
515.0	0	1	0	0
525.0	0	1	0	2
528.0	0	1	0	0
536.0	0	0	0	1
540.0	0	1	0	0
543.0	0	1	0	1
548.0	0	0	0	1
549.0	0	1	0	0
556.0	0	0	0	1
559.0	0	1	0	0
573.0	0	0	0	1
576.0	0	1	0	1
579.0	0	1	0	0
584.0	0	0	0	1
585.0	0	1	0	0
587.0	0	0	0	1
588.0	0	1	0	1
594.0	0	1	0	0
610.0	0	1	0	1
611.0	0	0	0	1
615.0	0	0	0	1
617.0	0	1	0	1
618.0	0	1	0	0
623.0	0	1	0	0
631.0	0	0	0	1
633.0	0	0	0	1
634.0	0	2	0	0
642.0	0	1	0	1
676.0	0	1	0	1
678.0	0	0	0	1
683.0	0	0	0	1
687.0	0	1	0	0
689.0	0	1	0	0
711.0	0	0	0	1
714.0	0	1	0	0
735.0	0	0	0	1
738.0	0	0	0	1
739.0	0	1	0	0
740.0	0	1	0	0
749.0	0	0	0	1
755.0	0	1	0	0
780.0	0	0	0	1
784.0	0	1	0	0
785.0	0	0	0	1
790.0	0	1	0	0
802.0	0	0	0	1
805.0	0	1	0	0
823.0	0	0	0	1
830.0	0	1	0	0
831.0	0	0	0	1
847.0	0	1	0	0
984.0	0	0	0	1
993.0	0	1	0	0
1050.0	0	0	0	1
1051.0	0	1	0	0
1106.0	0	1	0	1
1169.0	0	0	0	1
1175.0	0	1	0	0
1212.0	0	0	0	1
1217.0	0	1	0	0
1224.0	0	1	0	1
1226.0	0	0	0	1
1227.0	0	1	0	0
1271.0	0	0	0	1
1273.0	0	1	0	0
1288.0	0	0	0	1
1295.0	0	1	0	0
1325.0	0	0	0	1
1339.0	0	1	0	0
1346.0	0	0	0	1
1351.0	0	0	0	1
1355.0	0	1	0	0
1368.0	0	1	0	0
1392.0	0	0	0	1
1397.0	0	1	0	0
1430.0	0	0	0	1
1443.0	0	1	0	1
1444.0	0	1	0	0
1521.0	0	0	0	1
1532.0	0	1	0	1
1545.0	0	1	0	0
1558.0	0	0	0	1
1568.0	0	1	0	0
1724.0	0	0	0	1
1733.0	0	1	0	0
1841.0	0	0	0	1
1851.0	0	1	0	0
1855.0	0	0	0	1
1869.0	0	1	0	0
2173.0	0	0	0	1
2189.0	0	1	0	0
2249.0	0	0	0	1
2253.0	0	1	0	0
2734.0	0	0	0	1
2739.0	0	1	0	0
5644.0	0	0	0	1
5661.0	0	1	0	0
5953.0	0	0	0	1
5961.0	0	1	0	0
9157.0	0	0	0	1
9191.0	0	1	0	0
23260.0	0	0	0	1
23332.0	0	1	0	0