## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/RS_Mac_Zaj_1_2020-09-13/RS_Mac_Zaj_1_2020-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/RS_Mac_Zaj_1_2020-09-13/RS_Mac_Zaj_1_2020-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/RS_Mac_Zaj_1_2020-09-13/RS_Mac_Zaj_1_2020-09-13.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 Jan 19 08:37:34 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	3830776	21893474	0	0	1971697	3712460	178012	0.197334	59255331

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006777	14920269	0	15046145
2.0	1.702556	2457168	174538	2370949
3.0	2.183406	398603	1573	368322
4.0	2.515719	64419	24	56992
5.0	2.74538	10913	7	9397
6.0	2.904097	2222	2	1911
7.0	3.013786	839	3	748
8.0	3.089592	424	0	409
9.0	3.14198	295	4	288
10.0	3.178186	225	0	230
11.0	3.203208	139	1	129
12.0	3.2205	150	0	158
13.0	3.232451	117	0	116
14.0	3.24071	100	0	92
15.0	3.246418	83	1	83
16.0	3.250362	85	0	89
17.0	3.253088	74	0	69
18.0	3.254972	58	0	58
19.0	3.256274	53	0	54
20.0	3.257174	47	0	48
21.0	3.257796	40	0	38
22.0	3.258226	40	1	43
23.0	3.258523	36	0	35
24.0	3.258728	40	0	39
25.0	3.25887	36	0	36
26.0	3.258968	19	0	16
27.0	3.259036	14	0	16
28.0	3.259083	20	0	18
29.0	3.259115	21	0	21
30.0	3.259137	16	0	16
31.0	3.259153	14	0	14
32.0	3.259163	12	0	13
33.0	3.259171	20	0	21
34.0	3.259176	13	0	11
35.0	3.259179	15	0	15
36.0	3.259182	13	0	15
37.0	3.259184	9	0	10
38.0	3.259185	13	0	10
39.0	3.259186	10	0	12
40.0	3.259186	15	0	13
41.0	3.259186	10	0	11
42.0	3.259187	8	0	8
43.0	3.259187	12	0	11
44.0	3.259187	9	0	10
45.0	3.259187	11	0	13
46.0	3.259187	9	1	9
47.0	3.259187	11	0	11
48.0	3.259187	10	0	10
49.0	3.259187	16	0	15
50.0	3.259187	6	0	4
51.0	3.259187	6	0	6
52.0	3.259187	6	0	7
53.0	3.259187	4	0	5
54.0	3.259187	7	0	5
55.0	3.259187	5	0	6
56.0	3.259187	7	0	7
57.0	3.259187	9	0	10
58.0	3.259187	6	0	5
59.0	3.259187	6	0	6
60.0	3.259187	5	0	5
61.0	3.259187	6	0	7
62.0	3.259187	8	0	6
63.0	3.259187	3	0	3
64.0	3.259187	8	0	9
65.0	3.259187	4	0	6
66.0	3.259187	7	0	4
67.0	3.259187	4	0	5
68.0	3.259187	4	0	5
69.0	3.259187	5	0	4
70.0	3.259187	4	0	3
71.0	3.259187	3	0	3
72.0	3.259187	6	0	7
73.0	3.259187	6	0	6
74.0	3.259187	5	0	4
75.0	3.259187	4	0	6
76.0	3.259187	5	0	3
77.0	3.259187	4	0	4
78.0	3.259187	1	0	1
79.0	3.259187	5	1	6
80.0	3.259187	8	0	7
81.0	3.259187	3	0	3
82.0	3.259187	3	0	3
83.0	3.259187	3	0	3
84.0	3.259187	5	0	6
85.0	3.259187	3	0	2
86.0	3.259187	3	0	3
87.0	3.259187	3	0	3
88.0	3.259187	2	0	3
89.0	3.259187	3	0	3
90.0	3.259187	2	0	2
91.0	3.259187	2	0	5
92.0	3.259187	7	0	5
93.0	3.259187	2	0	2
94.0	3.259187	4	0	4
95.0	3.259187	1	0	0
96.0	3.259187	2	0	1
97.0	3.259187	2	0	2
98.0	3.259187	0	0	0
99.0	3.259187	3	0	3
100.0	3.259187	3	0	3
101.0	0	1	0	1
102.0	0	1	0	1
103.0	0	1	0	1
104.0	0	1	0	2
105.0	0	4	0	4
106.0	0	4	0	5
107.0	0	3	0	2
108.0	0	4	0	3
109.0	0	1	0	2
110.0	0	4	0	3
111.0	0	3	0	4
112.0	0	3	0	2
113.0	0	2	0	2
114.0	0	1	0	1
115.0	0	1	0	1
116.0	0	2	0	2
117.0	0	5	0	6
118.0	0	2	0	2
119.0	0	4	0	3
120.0	0	2	0	2
121.0	0	3	0	3
123.0	0	4	0	5
124.0	0	2	0	1
125.0	0	0	0	2
126.0	0	1	0	0
127.0	0	3	0	2
128.0	0	1	0	2
129.0	0	3	0	2
130.0	0	1	0	2
131.0	0	3	0	3
132.0	0	3	0	2
133.0	0	2	0	3
134.0	0	4	0	4
135.0	0	5	0	4
137.0	0	0	0	2
138.0	0	1	0	1
139.0	0	2	0	0
140.0	0	0	0	1
142.0	0	2	0	2
143.0	0	1	0	2
144.0	0	2	0	0
146.0	0	1	0	1
147.0	0	1	0	2
148.0	0	1	0	1
149.0	0	2	0	2
150.0	0	4	0	3
151.0	0	2	0	3
152.0	0	1	0	0
154.0	0	3	0	3
155.0	0	1	0	1
156.0	0	1	0	2
157.0	0	2	0	2
158.0	0	2	0	1
160.0	0	1	0	2
161.0	0	1	0	0
162.0	0	2	0	2
163.0	0	3	0	3
164.0	0	2	0	2
165.0	0	1	0	1
166.0	0	1	0	2
167.0	0	1	0	2
168.0	0	2	0	1
169.0	0	2	0	1
170.0	0	2	0	2
172.0	0	1	0	1
173.0	0	1	0	1
174.0	0	2	0	2
175.0	0	1	0	1
176.0	0	1	0	2
177.0	0	2	0	2
178.0	0	3	0	2
180.0	0	3	0	3
181.0	0	1	0	1
182.0	0	2	0	2
183.0	0	1	0	2
184.0	0	2	0	2
185.0	0	1	0	0
186.0	0	2	0	2
188.0	0	1	0	1
189.0	0	2	0	2
191.0	0	1	0	2
193.0	0	1	0	0
195.0	0	1	0	1
196.0	0	2	0	2
200.0	0	1	0	1
202.0	0	0	0	1
204.0	0	1	0	0
205.0	0	1	0	1
206.0	0	0	0	1
207.0	0	3	0	2
209.0	0	0	0	1
210.0	0	1	0	0
215.0	0	1	0	1
217.0	0	1	0	1
221.0	0	1	0	2
222.0	0	2	0	2
223.0	0	2	0	1
225.0	0	1	0	1
226.0	0	1	0	1
229.0	0	1	0	1
230.0	0	0	0	1
231.0	0	1	0	1
234.0	0	3	0	2
236.0	0	2	0	2
237.0	0	1	0	1
238.0	0	1	0	1
240.0	0	1	0	1
241.0	0	1	0	1
243.0	0	1	0	1
244.0	0	1	0	1
252.0	0	1	0	1
253.0	0	1	0	1
254.0	0	1	0	1
257.0	0	1	0	1
279.0	0	0	0	1
281.0	0	1	0	0
282.0	0	0	0	1
283.0	0	1	0	1
285.0	0	1	0	0
286.0	0	0	0	1
287.0	0	2	0	1
290.0	0	0	0	1
291.0	0	1	0	0
292.0	0	0	0	1
293.0	0	0	0	1
294.0	0	2	0	0
300.0	0	0	0	1
302.0	0	1	0	0
310.0	0	1	0	1
313.0	0	1	0	1
314.0	0	0	0	1
315.0	0	1	0	0
319.0	0	1	0	1
321.0	0	0	0	1
322.0	0	1	0	0
329.0	0	1	0	1
330.0	0	1	0	2
334.0	0	2	0	1
335.0	0	1	0	1
345.0	0	1	0	1
353.0	0	2	0	2
358.0	0	1	0	1
360.0	0	1	0	1
361.0	0	1	0	2
363.0	0	1	0	1
364.0	0	1	0	1
365.0	0	1	0	0
370.0	0	0	0	2
371.0	0	0	0	1
372.0	0	2	0	0
374.0	0	1	0	0
377.0	0	0	0	1
378.0	0	1	0	0
379.0	0	1	0	1
382.0	0	1	0	1
384.0	0	1	0	1
388.0	0	0	0	1
390.0	0	1	0	0
391.0	0	0	0	1
392.0	0	2	0	2
393.0	0	0	0	1
394.0	0	2	0	0
395.0	0	1	0	1
399.0	0	1	0	1
405.0	0	0	0	1
407.0	0	1	0	1
408.0	0	1	0	0
412.0	0	0	0	1
414.0	0	1	0	0
417.0	0	0	0	1
419.0	0	1	0	2
420.0	0	1	0	0
422.0	0	1	0	0
430.0	0	0	0	1
432.0	0	1	0	0
435.0	0	1	0	2
437.0	0	1	0	0
440.0	0	0	0	2
441.0	0	3	0	2
442.0	0	2	0	1
445.0	0	0	0	1
446.0	0	1	0	1
447.0	0	1	0	0
450.0	0	1	0	1
459.0	0	1	0	1
479.0	0	1	0	1
487.0	0	0	0	2
490.0	0	1	0	0
493.0	0	0	0	1
495.0	0	1	0	0
496.0	0	1	0	0
510.0	0	1	0	1
524.0	0	1	0	1
532.0	0	1	0	1
539.0	0	2	0	2
540.0	0	1	0	1
543.0	0	0	0	1
545.0	0	1	0	0
551.0	0	0	0	1
553.0	0	1	0	0
597.0	0	1	0	1
598.0	0	0	0	1
600.0	0	1	0	0
607.0	0	1	0	1
632.0	0	0	0	1
634.0	0	1	0	0
652.0	0	1	0	1
653.0	0	1	0	1
711.0	0	0	0	1
714.0	0	1	0	0
718.0	0	0	0	1
723.0	0	1	0	0
726.0	0	0	0	1
730.0	0	1	0	0
759.0	0	1	0	1
791.0	0	1	0	1
937.0	0	0	0	1
939.0	0	1	0	0
951.0	0	0	0	1
954.0	0	1	0	0
960.0	0	0	0	1
968.0	0	1	0	0
988.0	0	0	0	1
989.0	0	0	0	1
990.0	0	1	0	1
993.0	0	1	0	0
996.0	0	1	0	0
1006.0	0	0	0	1
1016.0	0	1	0	0
1058.0	0	0	0	1
1064.0	0	1	0	0
1094.0	0	0	0	1
1098.0	0	1	0	0
1115.0	0	0	0	1
1117.0	0	1	0	0
1141.0	0	0	0	1
1142.0	0	1	0	0
1150.0	0	0	0	1
1153.0	0	0	0	1
1158.0	0	1	0	0
1159.0	0	1	0	0
1171.0	0	0	0	1
1173.0	0	1	0	0
1217.0	0	0	0	1
1222.0	0	1	0	0
1245.0	0	0	0	1
1249.0	0	1	0	0
1289.0	0	0	0	1
1290.0	0	1	0	0
1492.0	0	0	0	1
1493.0	0	1	0	1
1494.0	0	1	0	0
1544.0	0	0	0	1
1547.0	0	1	0	0
2074.0	0	0	0	1
2088.0	0	1	0	0
2518.0	0	0	0	1
2519.0	0	1	0	0
3362.0	0	0	0	1
3366.0	0	1	0	0
6450.0	0	0	0	1
6456.0	0	1	0	0
8245.0	0	0	0	1
8266.0	0	1	0	0
12396.0	0	0	0	1
12441.0	0	1	0	0
30095.0	0	0	0	1
30173.0	0	1	0	0