## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/IT_Tre_San_1_2021-06-28/IT_Tre_San_1_2021-06-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/IT_Tre_San_1_2021-06-28/IT_Tre_San_1_2021-06-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/IT_Tre_San_1_2021-06-28/IT_Tre_San_1_2021-06-28.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 Jan 18 04:30:04 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	5466995	24567022	0	0	2856408	6884068	239340	0.304473	35989801

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006862	12345920	0	12468260
2.0	1.515625	3519625	232878	3469173
3.0	1.772702	959479	2843	917071
4.0	1.902601	249089	69	229540
5.0	1.968239	62374	25	55532
6.0	2.001406	15471	11	13310
7.0	2.018164	4225	6	3552
8.0	2.026633	1403	5	1238
9.0	2.030912	660	3	624
10.0	2.033074	471	2	434
11.0	2.034166	339	2	343
12.0	2.034718	264	2	259
13.0	2.034997	205	1	202
14.0	2.035138	180	1	187
15.0	2.035209	155	0	149
16.0	2.035245	134	1	134
17.0	2.035264	116	0	114
18.0	2.035273	109	1	108
19.0	2.035277	105	2	110
20.0	2.03528	87	0	80
21.0	2.035281	88	0	89
22.0	2.035282	74	0	69
23.0	2.035282	65	0	73
24.0	2.035282	72	0	70
25.0	2.035282	63	0	60
26.0	2.035282	52	0	49
27.0	2.035282	41	0	40
28.0	2.035282	51	0	56
29.0	2.035282	43	0	39
30.0	2.035282	37	0	33
31.0	2.035282	36	0	43
32.0	2.035282	33	0	30
33.0	2.035282	29	0	27
34.0	2.035282	41	0	41
35.0	2.035282	32	0	36
36.0	2.035282	21	0	21
37.0	2.035282	21	0	17
38.0	2.035282	22	2	20
39.0	2.035282	17	0	19
40.0	2.035282	22	0	22
41.0	2.035282	19	0	19
42.0	2.035282	16	0	24
43.0	2.035282	26	0	22
44.0	2.035282	22	0	22
45.0	2.035282	18	0	16
46.0	2.035282	20	0	18
47.0	2.035282	20	0	21
48.0	2.035282	15	0	12
49.0	2.035282	12	0	14
50.0	2.035282	17	0	16
51.0	2.035282	11	0	11
52.0	2.035282	14	0	14
53.0	2.035282	15	0	15
54.0	2.035282	10	0	10
55.0	2.035282	13	0	14
56.0	2.035282	15	0	14
57.0	2.035282	8	0	10
58.0	2.035282	12	0	8
59.0	2.035282	14	0	18
60.0	2.035282	12	0	8
61.0	2.035282	10	0	10
62.0	2.035282	6	0	10
63.0	2.035282	14	0	13
64.0	2.035282	8	0	7
65.0	2.035282	7	0	5
66.0	2.035282	8	0	8
67.0	2.035282	4	0	4
68.0	2.035282	6	0	6
69.0	2.035282	6	0	9
70.0	2.035282	10	0	9
71.0	2.035282	7	0	7
72.0	2.035282	10	0	10
73.0	2.035282	10	0	11
74.0	2.035282	8	0	7
75.0	2.035282	6	0	4
76.0	2.035282	6	0	7
77.0	2.035282	6	0	8
78.0	2.035282	9	0	9
79.0	2.035282	6	0	5
80.0	2.035282	11	0	10
81.0	2.035282	4	0	5
82.0	2.035282	6	0	6
83.0	2.035282	6	0	5
84.0	2.035282	4	0	4
85.0	2.035282	4	0	7
86.0	2.035282	9	0	7
87.0	2.035282	7	0	6
88.0	2.035282	5	0	6
89.0	2.035282	5	0	4
90.0	2.035282	5	0	4
91.0	2.035282	2	0	3
92.0	2.035282	4	0	6
93.0	2.035282	4	1	3
94.0	2.035282	2	0	1
95.0	2.035282	6	0	5
96.0	2.035282	4	0	5
97.0	2.035282	2	0	3
98.0	2.035282	4	0	3
99.0	2.035282	3	0	2
100.0	2.035282	3	0	4
101.0	0	6	0	6
102.0	0	6	0	6
103.0	0	1	0	2
104.0	0	3	0	2
105.0	0	5	0	5
106.0	0	7	0	7
107.0	0	4	0	7
108.0	0	5	0	2
109.0	0	3	0	4
110.0	0	3	0	4
111.0	0	9	0	8
112.0	0	3	0	5
113.0	0	4	0	2
114.0	0	4	0	3
115.0	0	3	0	2
116.0	0	2	0	2
117.0	0	2	0	2
118.0	0	4	0	4
119.0	0	2	0	2
120.0	0	7	0	7
121.0	0	3	0	3
122.0	0	2	0	4
123.0	0	4	0	5
124.0	0	7	0	5
125.0	0	2	0	4
126.0	0	3	0	1
127.0	0	3	0	2
128.0	0	3	0	4
129.0	0	1	0	2
130.0	0	4	0	5
131.0	0	5	0	4
132.0	0	3	0	5
133.0	0	6	0	5
134.0	0	4	0	2
135.0	0	3	0	4
136.0	0	2	0	5
137.0	0	7	0	8
138.0	0	7	0	6
139.0	0	4	0	2
140.0	0	3	0	2
141.0	0	4	0	2
142.0	0	2	0	2
144.0	0	1	0	1
145.0	0	2	0	3
146.0	0	1	0	1
147.0	0	3	0	3
148.0	0	1	0	2
149.0	0	3	0	3
150.0	0	2	0	0
151.0	0	2	0	2
152.0	0	3	0	3
153.0	0	1	0	2
154.0	0	3	0	5
155.0	0	3	0	2
156.0	0	1	0	3
157.0	0	5	0	2
158.0	0	1	0	1
159.0	0	2	0	1
161.0	0	2	0	3
162.0	0	0	0	1
163.0	0	1	0	0
164.0	0	2	0	2
165.0	0	1	0	0
166.0	0	1	0	1
167.0	0	1	0	3
168.0	0	2	0	1
169.0	0	1	0	2
170.0	0	2	0	1
171.0	0	1	0	0
172.0	0	1	0	1
173.0	0	3	0	3
174.0	0	1	0	2
175.0	0	2	0	3
176.0	0	1	0	0
177.0	0	1	0	3
178.0	0	2	0	2
179.0	0	3	0	1
180.0	0	4	0	4
181.0	0	2	0	3
183.0	0	4	0	2
184.0	0	1	0	1
185.0	0	1	0	3
186.0	0	2	0	2
187.0	0	1	0	0
188.0	0	1	0	0
189.0	0	1	0	2
190.0	0	1	0	1
191.0	0	2	0	1
192.0	0	1	0	1
193.0	0	2	0	2
195.0	0	0	0	1
196.0	0	0	0	1
197.0	0	2	0	3
198.0	0	1	0	2
199.0	0	4	0	1
200.0	0	2	0	2
201.0	0	0	0	1
202.0	0	2	0	2
203.0	0	2	0	1
204.0	0	4	0	3
205.0	0	1	0	2
208.0	0	3	0	2
209.0	0	4	0	4
210.0	0	2	0	2
211.0	0	1	0	4
212.0	0	3	0	1
213.0	0	3	0	2
214.0	0	0	0	1
215.0	0	1	0	0
216.0	0	1	0	1
217.0	0	2	0	2
218.0	0	2	0	3
219.0	0	3	0	3
220.0	0	1	0	0
221.0	0	1	0	2
222.0	0	0	0	1
223.0	0	1	0	2
224.0	0	3	0	1
225.0	0	2	0	1
226.0	0	1	0	2
227.0	0	2	0	2
229.0	0	3	0	2
230.0	0	1	0	1
232.0	0	1	0	2
233.0	0	2	0	1
235.0	0	0	0	1
236.0	0	2	0	3
237.0	0	1	0	0
238.0	0	1	0	0
242.0	0	0	0	1
243.0	0	1	0	1
244.0	0	2	0	1
245.0	0	0	0	1
249.0	0	1	0	0
251.0	0	1	0	2
253.0	0	1	0	0
254.0	0	0	0	1
255.0	0	1	0	1
256.0	0	0	0	1
257.0	0	2	0	1
258.0	0	0	0	2
259.0	0	1	0	0
260.0	0	0	0	1
261.0	0	3	0	1
262.0	0	2	0	4
263.0	0	2	0	0
264.0	0	2	0	2
265.0	0	1	0	0
267.0	0	0	0	1
268.0	0	1	0	0
269.0	0	1	0	1
270.0	0	3	0	4
272.0	0	1	0	1
273.0	0	0	0	1
274.0	0	2	0	0
279.0	0	1	0	1
280.0	0	0	0	1
281.0	0	0	0	1
282.0	0	1	0	1
283.0	0	2	0	1
284.0	0	1	0	0
287.0	0	0	0	1
288.0	0	0	0	1
289.0	0	1	0	0
290.0	0	0	0	1
291.0	0	1	0	0
292.0	0	3	0	2
296.0	0	2	0	3
297.0	0	1	0	1
299.0	0	1	0	0
300.0	0	1	0	2
301.0	0	2	0	1
302.0	0	0	0	1
304.0	0	0	0	1
305.0	0	1	0	1
306.0	0	0	0	1
308.0	0	3	0	0
309.0	0	0	0	1
310.0	0	0	0	2
311.0	0	2	0	1
312.0	0	1	0	0
313.0	0	0	0	2
314.0	0	1	0	0
315.0	0	3	0	2
316.0	0	1	0	0
318.0	0	1	0	1
324.0	0	0	0	1
325.0	0	2	0	1
326.0	0	1	0	1
327.0	0	2	0	2
329.0	0	2	0	2
330.0	0	1	0	1
331.0	0	0	0	1
332.0	0	3	0	2
334.0	0	1	0	1
335.0	0	0	0	1
338.0	0	2	0	1
339.0	0	1	0	1
342.0	0	1	0	1
350.0	0	1	0	1
356.0	0	0	0	1
357.0	0	1	0	1
358.0	0	1	0	0
361.0	0	2	0	2
365.0	0	1	0	2
366.0	0	1	0	0
370.0	0	1	0	1
375.0	0	1	0	1
379.0	0	0	0	1
381.0	0	0	0	1
382.0	0	1	0	0
383.0	0	2	0	2
385.0	0	1	0	0
397.0	0	1	0	1
400.0	0	0	0	1
402.0	0	1	0	0
403.0	0	1	0	1
406.0	0	0	0	1
407.0	0	1	0	0
409.0	0	0	0	1
410.0	0	1	0	0
412.0	0	1	0	2
415.0	0	1	0	0
417.0	0	0	0	1
418.0	0	1	0	0
419.0	0	0	0	1
422.0	0	1	0	0
423.0	0	1	0	1
428.0	0	0	0	1
432.0	0	1	0	1
433.0	0	1	0	0
439.0	0	0	0	1
441.0	0	2	0	1
443.0	0	1	0	1
445.0	0	0	0	1
448.0	0	1	0	0
451.0	0	1	0	1
453.0	0	1	0	1
456.0	0	0	0	1
457.0	0	0	0	1
458.0	0	1	0	1
459.0	0	1	0	0
460.0	0	1	0	1
461.0	0	1	0	0
462.0	0	1	0	1
464.0	0	1	0	2
465.0	0	0	0	1
466.0	0	2	0	0
467.0	0	0	0	1
472.0	0	1	0	0
474.0	0	0	0	1
476.0	0	1	0	1
478.0	0	1	0	0
483.0	0	0	0	1
485.0	0	0	0	1
486.0	0	1	0	1
487.0	0	1	0	1
488.0	0	1	0	0
489.0	0	1	0	0
490.0	0	0	0	1
492.0	0	1	0	0
494.0	0	0	0	1
495.0	0	1	0	0
497.0	0	2	0	2
502.0	0	0	0	1
504.0	0	1	0	2
505.0	0	1	0	1
506.0	0	1	0	0
507.0	0	1	0	0
509.0	0	1	0	1
517.0	0	1	0	1
524.0	0	0	0	1
527.0	0	1	0	0
542.0	0	0	0	1
543.0	0	1	0	1
545.0	0	1	0	0
547.0	0	0	0	1
549.0	0	1	0	0
554.0	0	0	0	1
558.0	0	1	0	0
566.0	0	0	0	1
568.0	0	1	0	0
569.0	0	1	0	1
570.0	0	0	0	1
571.0	0	0	0	1
573.0	0	1	0	0
574.0	0	1	0	0
590.0	0	1	0	1
594.0	0	0	0	1
600.0	0	1	0	0
602.0	0	0	0	1
605.0	0	0	0	1
606.0	0	1	0	0
607.0	0	1	0	0
609.0	0	0	0	1
610.0	0	0	0	1
611.0	0	2	0	0
615.0	0	0	0	2
619.0	0	1	0	0
620.0	0	1	0	0
621.0	0	0	0	1
624.0	0	1	0	0
630.0	0	0	0	1
632.0	0	1	0	1
636.0	0	1	0	0
647.0	0	0	0	2
650.0	0	1	0	0
651.0	0	1	0	0
664.0	0	1	0	1
665.0	0	0	0	1
669.0	0	1	0	0
672.0	0	1	0	1
675.0	0	0	0	1
679.0	0	1	0	0
688.0	0	0	0	1
690.0	0	1	0	0
727.0	0	0	0	1
728.0	0	1	0	0
736.0	0	0	0	1
738.0	0	1	0	1
743.0	0	1	0	0
745.0	0	1	0	1
747.0	0	0	0	1
751.0	0	0	0	1
752.0	0	1	0	0
754.0	0	1	0	0
770.0	0	0	0	1
771.0	0	1	0	0
773.0	0	0	0	1
777.0	0	1	0	0
781.0	0	0	0	1
789.0	0	1	0	1
796.0	0	1	0	0
801.0	0	0	0	1
803.0	0	1	0	1
804.0	0	0	0	1
807.0	0	1	0	0
808.0	0	1	0	0
816.0	0	0	0	1
820.0	0	1	0	0
839.0	0	0	0	1
844.0	0	1	0	0
852.0	0	1	0	1
925.0	0	0	0	1
930.0	0	0	0	1
932.0	0	1	0	0
933.0	0	1	0	0
946.0	0	0	0	1
950.0	0	1	0	0
965.0	0	0	0	1
970.0	0	1	0	0
972.0	0	0	0	1
974.0	0	0	0	1
975.0	0	1	0	0
979.0	0	1	0	0
980.0	0	0	0	1
987.0	0	1	0	0
1016.0	0	1	0	1
1045.0	0	0	0	1
1052.0	0	1	0	0
1059.0	0	0	0	1
1065.0	0	1	0	0
1095.0	0	0	0	1
1101.0	0	1	0	0
1138.0	0	0	0	1
1149.0	0	1	0	0
1164.0	0	0	0	1
1170.0	0	1	0	1
1173.0	0	1	0	0
1182.0	0	0	0	1
1185.0	0	1	0	0
1190.0	0	0	0	1
1194.0	0	1	0	0
1249.0	0	0	0	1
1253.0	0	1	0	0
1254.0	0	0	0	1
1258.0	0	1	0	0
1350.0	0	0	0	1
1352.0	0	1	0	0
1360.0	0	0	0	1
1363.0	0	1	0	0
1377.0	0	0	0	1
1380.0	0	1	0	0
1386.0	0	0	0	1
1391.0	0	1	0	0
1461.0	0	0	0	1
1471.0	0	1	0	0
1483.0	0	0	0	1
1492.0	0	1	0	0
1524.0	0	0	0	1
1532.0	0	2	0	1
1550.0	0	0	0	1
1556.0	0	1	0	0
1594.0	0	0	0	1
1595.0	0	1	0	0
1631.0	0	0	0	1
1642.0	0	1	0	0
1649.0	0	0	0	1
1657.0	0	1	0	0
1737.0	0	0	0	1
1739.0	0	1	0	0
1761.0	0	1	0	1
1786.0	0	0	0	1
1787.0	0	1	0	0
1865.0	0	0	0	1
1878.0	0	1	0	0
1940.0	0	0	0	1
1952.0	0	1	0	0
2498.0	0	0	0	1
2513.0	0	1	0	0
2634.0	0	0	0	1
2651.0	0	1	0	0
2897.0	0	0	0	1
2898.0	0	1	0	0
3038.0	0	0	0	1
3056.0	0	1	0	0
3583.0	0	0	0	1
3592.0	0	1	0	0
3715.0	0	0	0	1
3752.0	0	1	0	0
7667.0	0	0	0	1
7685.0	0	1	0	0
7848.0	0	0	0	1
7858.0	0	1	0	0
13627.0	0	0	0	1
13664.0	0	1	0	0
30252.0	0	0	0	1
30344.0	0	1	0	0