## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT 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 Sep 22 21:33:31 CEST 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
Unknown Library	898159	37374043	0	1054413	639840	5912935	0	0.16479	105298003

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	29004674	29004674
2.0	1.701218	1723592	1723592
3.0	2.192926	327145	327145
4.0	2.53772	135104	135104
5.0	2.779496	73214	73214
6.0	2.949033	45228	45228
7.0	3.067916	30370	30370
8.0	3.151279	21502	21502
9.0	3.209735	15789	15789
10.0	3.250725	11950	11950
11.0	3.279468	9348	9348
12.0	3.299623	7645	7645
13.0	3.313757	6078	6078
14.0	3.323667	5120	5120
15.0	3.330616	4238	4238
16.0	3.335489	3578	3578
17.0	3.338906	3040	3040
18.0	3.341303	2687	2687
19.0	3.342983	2328	2328
20.0	3.344161	2063	2063
21.0	3.344987	1751	1751
22.0	3.345566	1553	1553
23.0	3.345973	1409	1409
24.0	3.346258	1261	1261
25.0	3.346457	1210	1210
26.0	3.346597	1011	1011
27.0	3.346696	946	946
28.0	3.346764	878	878
29.0	3.346813	825	825
30.0	3.346847	701	701
31.0	3.34687	688	688
32.0	3.346887	628	628
33.0	3.346899	591	591
34.0	3.346907	567	567
35.0	3.346913	522	522
36.0	3.346917	469	469
37.0	3.346919	461	461
38.0	3.346921	397	397
39.0	3.346923	380	380
40.0	3.346924	357	357
41.0	3.346924	331	331
42.0	3.346925	300	300
43.0	3.346925	324	324
44.0	3.346926	279	279
45.0	3.346926	295	295
46.0	3.346926	264	264
47.0	3.346926	235	235
48.0	3.346926	224	224
49.0	3.346926	240	240
50.0	3.346926	231	231
51.0	3.346926	219	219
52.0	3.346926	178	178
53.0	3.346926	200	200
54.0	3.346926	172	172
55.0	3.346926	168	168
56.0	3.346926	153	153
57.0	3.346926	146	146
58.0	3.346926	147	147
59.0	3.346926	143	143
60.0	3.346926	141	141
61.0	3.346926	139	139
62.0	3.346926	111	111
63.0	3.346926	120	120
64.0	3.346926	106	106
65.0	3.346926	108	108
66.0	3.346926	99	99
67.0	3.346926	119	119
68.0	3.346926	100	100
69.0	3.346926	84	84
70.0	3.346926	108	108
71.0	3.346926	87	87
72.0	3.346926	95	95
73.0	3.346926	85	85
74.0	3.346926	83	83
75.0	3.346926	86	86
76.0	3.346926	58	58
77.0	3.346926	69	69
78.0	3.346926	72	72
79.0	3.346926	72	72
80.0	3.346926	68	68
81.0	3.346926	65	65
82.0	3.346926	64	64
83.0	3.346926	54	54
84.0	3.346926	61	61
85.0	3.346926	57	57
86.0	3.346926	55	55
87.0	3.346926	50	50
88.0	3.346926	34	34
89.0	3.346926	45	45
90.0	3.346926	54	54
91.0	3.346926	53	53
92.0	3.346926	44	44
93.0	3.346926	48	48
94.0	3.346926	34	34
95.0	3.346926	44	44
96.0	3.346926	43	43
97.0	3.346926	36	36
98.0	3.346926	34	34
99.0	3.346926	44	44
100.0	3.346926	45	45
101.0	0	34	34
102.0	0	42	42
103.0	0	38	38
104.0	0	35	35
105.0	0	37	37
106.0	0	45	45
107.0	0	35	35
108.0	0	36	36
109.0	0	26	26
110.0	0	27	27
111.0	0	33	33
112.0	0	33	33
113.0	0	22	22
114.0	0	34	34
115.0	0	36	36
116.0	0	18	18
117.0	0	31	31
118.0	0	27	27
119.0	0	25	25
120.0	0	32	32
121.0	0	28	28
122.0	0	20	20
123.0	0	18	18
124.0	0	22	22
125.0	0	20	20
126.0	0	27	27
127.0	0	20	20
128.0	0	22	22
129.0	0	21	21
130.0	0	25	25
131.0	0	11	11
132.0	0	11	11
133.0	0	25	25
134.0	0	18	18
135.0	0	19	19
136.0	0	22	22
137.0	0	18	18
138.0	0	25	25
139.0	0	23	23
140.0	0	15	15
141.0	0	14	14
142.0	0	20	20
143.0	0	17	17
144.0	0	12	12
145.0	0	18	18
146.0	0	15	15
147.0	0	14	14
148.0	0	11	11
149.0	0	11	11
150.0	0	20	20
151.0	0	14	14
152.0	0	15	15
153.0	0	13	13
154.0	0	9	9
155.0	0	10	10
156.0	0	9	9
157.0	0	15	15
158.0	0	9	9
159.0	0	9	9
160.0	0	14	14
161.0	0	11	11
162.0	0	4	4
163.0	0	9	9
164.0	0	8	8
165.0	0	17	17
166.0	0	8	8
167.0	0	14	14
168.0	0	13	13
169.0	0	14	14
170.0	0	7	7
171.0	0	5	5
172.0	0	12	12
173.0	0	13	13
174.0	0	10	10
175.0	0	12	12
176.0	0	7	7
177.0	0	8	8
178.0	0	12	12
179.0	0	15	15
180.0	0	10	10
181.0	0	9	9
182.0	0	12	12
183.0	0	7	7
184.0	0	10	10
185.0	0	6	6
186.0	0	13	13
187.0	0	17	17
188.0	0	12	12
189.0	0	7	7
190.0	0	5	5
191.0	0	10	10
192.0	0	3	3
193.0	0	6	6
194.0	0	10	10
195.0	0	4	4
196.0	0	11	11
197.0	0	8	8
198.0	0	5	5
199.0	0	8	8
200.0	0	5	5
201.0	0	7	7
202.0	0	7	7
203.0	0	6	6
204.0	0	11	11
205.0	0	6	6
206.0	0	3	3
207.0	0	2	2
208.0	0	6	6
209.0	0	11	11
210.0	0	7	7
211.0	0	6	6
212.0	0	7	7
213.0	0	10	10
214.0	0	8	8
215.0	0	6	6
216.0	0	5	5
217.0	0	4	4
218.0	0	6	6
219.0	0	3	3
220.0	0	5	5
221.0	0	3	3
222.0	0	6	6
223.0	0	8	8
224.0	0	4	4
225.0	0	9	9
226.0	0	5	5
227.0	0	8	8
228.0	0	6	6
229.0	0	4	4
230.0	0	7	7
231.0	0	3	3
232.0	0	6	6
233.0	0	7	7
234.0	0	4	4
235.0	0	8	8
236.0	0	6	6
237.0	0	2	2
238.0	0	6	6
239.0	0	2	2
240.0	0	8	8
241.0	0	7	7
242.0	0	10	10
243.0	0	3	3
244.0	0	7	7
245.0	0	2	2
246.0	0	6	6
247.0	0	5	5
248.0	0	4	4
249.0	0	8	8
250.0	0	2	2
251.0	0	3	3
252.0	0	7	7
253.0	0	4	4
254.0	0	6	6
255.0	0	2	2
256.0	0	6	6
257.0	0	6	6
258.0	0	3	3
259.0	0	2	2
260.0	0	3	3
261.0	0	7	7
263.0	0	2	2
264.0	0	2	2
265.0	0	1	1
266.0	0	5	5
267.0	0	4	4
268.0	0	3	3
269.0	0	2	2
270.0	0	1	1
271.0	0	5	5
272.0	0	6	6
273.0	0	8	8
274.0	0	2	2
275.0	0	1	1
276.0	0	3	3
277.0	0	3	3
278.0	0	3	3
279.0	0	7	7
280.0	0	3	3
281.0	0	5	5
282.0	0	3	3
284.0	0	4	4
285.0	0	6	6
286.0	0	2	2
287.0	0	5	5
288.0	0	7	7
289.0	0	4	4
290.0	0	4	4
291.0	0	6	6
292.0	0	3	3
293.0	0	5	5
294.0	0	4	4
295.0	0	2	2
296.0	0	3	3
297.0	0	2	2
298.0	0	2	2
299.0	0	3	3
300.0	0	2	2
301.0	0	3	3
302.0	0	2	2
304.0	0	3	3
305.0	0	2	2
306.0	0	2	2
307.0	0	3	3
309.0	0	2	2
310.0	0	1	1
311.0	0	2	2
313.0	0	1	1
315.0	0	2	2
317.0	0	2	2
318.0	0	3	3
319.0	0	3	3
320.0	0	2	2
321.0	0	3	3
323.0	0	1	1
325.0	0	1	1
326.0	0	2	2
327.0	0	3	3
328.0	0	2	2
329.0	0	1	1
330.0	0	1	1
331.0	0	3	3
332.0	0	2	2
333.0	0	6	6
335.0	0	4	4
336.0	0	2	2
337.0	0	3	3
338.0	0	3	3
339.0	0	3	3
340.0	0	2	2
341.0	0	3	3
342.0	0	2	2
343.0	0	2	2
344.0	0	3	3
346.0	0	2	2
347.0	0	3	3
349.0	0	4	4
350.0	0	2	2
351.0	0	2	2
352.0	0	1	1
353.0	0	6	6
354.0	0	1	1
355.0	0	1	1
356.0	0	1	1
357.0	0	2	2
358.0	0	2	2
359.0	0	4	4
361.0	0	2	2
363.0	0	1	1
364.0	0	3	3
365.0	0	3	3
366.0	0	2	2
367.0	0	1	1
369.0	0	2	2
370.0	0	1	1
371.0	0	2	2
373.0	0	3	3
374.0	0	1	1
375.0	0	2	2
376.0	0	2	2
377.0	0	2	2
378.0	0	3	3
379.0	0	2	2
380.0	0	3	3
381.0	0	2	2
382.0	0	2	2
383.0	0	1	1
384.0	0	3	3
385.0	0	3	3
386.0	0	1	1
389.0	0	1	1
391.0	0	3	3
392.0	0	1	1
397.0	0	4	4
398.0	0	2	2
399.0	0	4	4
400.0	0	2	2
402.0	0	1	1
404.0	0	1	1
405.0	0	1	1
406.0	0	2	2
407.0	0	1	1
408.0	0	1	1
409.0	0	1	1
412.0	0	2	2
414.0	0	1	1
415.0	0	1	1
417.0	0	1	1
419.0	0	2	2
421.0	0	1	1
422.0	0	1	1
423.0	0	2	2
424.0	0	1	1
425.0	0	1	1
427.0	0	3	3
428.0	0	3	3
430.0	0	1	1
432.0	0	1	1
434.0	0	1	1
437.0	0	1	1
438.0	0	1	1
442.0	0	2	2
443.0	0	2	2
444.0	0	1	1
445.0	0	1	1
447.0	0	3	3
448.0	0	1	1
454.0	0	1	1
456.0	0	1	1
457.0	0	1	1
463.0	0	2	2
464.0	0	1	1
468.0	0	2	2
469.0	0	1	1
470.0	0	1	1
473.0	0	1	1
475.0	0	1	1
476.0	0	2	2
480.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
486.0	0	1	1
489.0	0	1	1
490.0	0	1	1
492.0	0	1	1
494.0	0	1	1
495.0	0	1	1
496.0	0	1	1
497.0	0	2	2
499.0	0	1	1
501.0	0	1	1
502.0	0	1	1
511.0	0	1	1
512.0	0	1	1
514.0	0	2	2
517.0	0	1	1
518.0	0	2	2
522.0	0	1	1
525.0	0	1	1
529.0	0	1	1
532.0	0	2	2
533.0	0	1	1
535.0	0	1	1
539.0	0	1	1
540.0	0	1	1
542.0	0	1	1
548.0	0	1	1
552.0	0	1	1
553.0	0	1	1
558.0	0	2	2
560.0	0	2	2
564.0	0	1	1
568.0	0	2	2
572.0	0	1	1
575.0	0	1	1
576.0	0	1	1
578.0	0	1	1
580.0	0	1	1
589.0	0	1	1
591.0	0	1	1
594.0	0	1	1
595.0	0	1	1
598.0	0	1	1
604.0	0	1	1
606.0	0	2	2
607.0	0	1	1
617.0	0	1	1
619.0	0	1	1
623.0	0	2	2
624.0	0	1	1
633.0	0	1	1
636.0	0	1	1
637.0	0	1	1
638.0	0	1	1
639.0	0	1	1
641.0	0	1	1
644.0	0	1	1
653.0	0	1	1
656.0	0	1	1
657.0	0	2	2
661.0	0	1	1
666.0	0	1	1
671.0	0	1	1
674.0	0	1	1
677.0	0	2	2
679.0	0	1	1
680.0	0	1	1
686.0	0	2	2
689.0	0	1	1
692.0	0	1	1
695.0	0	1	1
696.0	0	1	1
697.0	0	1	1
711.0	0	1	1
714.0	0	1	1
715.0	0	1	1
716.0	0	1	1
721.0	0	1	1
722.0	0	1	1
741.0	0	1	1
747.0	0	1	1
752.0	0	1	1
759.0	0	1	1
760.0	0	1	1
767.0	0	1	1
775.0	0	1	1
777.0	0	2	2
780.0	0	1	1
790.0	0	1	1
797.0	0	1	1
801.0	0	1	1
803.0	0	1	1
804.0	0	1	1
823.0	0	1	1
824.0	0	1	1
825.0	0	1	1
830.0	0	1	1
834.0	0	1	1
835.0	0	1	1
840.0	0	1	1
844.0	0	1	1
845.0	0	1	1
846.0	0	1	1
848.0	0	1	1
849.0	0	1	1
853.0	0	1	1
858.0	0	1	1
869.0	0	1	1
875.0	0	1	1
878.0	0	1	1
880.0	0	1	1
886.0	0	1	1
909.0	0	1	1
914.0	0	1	1
918.0	0	1	1
924.0	0	1	1
925.0	0	1	1
934.0	0	1	1
941.0	0	1	1
956.0	0	1	1
957.0	0	1	1
979.0	0	1	1
1006.0	0	1	1
1016.0	0	1	1
1032.0	0	1	1
1046.0	0	1	1
1049.0	0	2	2
1053.0	0	1	1
1059.0	0	1	1
1061.0	0	1	1
1063.0	0	1	1
1069.0	0	1	1
1083.0	0	1	1
1084.0	0	1	1
1092.0	0	1	1
1101.0	0	1	1
1105.0	0	1	1
1115.0	0	1	1
1116.0	0	1	1
1133.0	0	1	1
1171.0	0	1	1
1213.0	0	2	2
1222.0	0	1	1
1223.0	0	1	1
1261.0	0	1	1
1263.0	0	1	1
1288.0	0	1	1
1346.0	0	1	1
1351.0	0	1	1
1388.0	0	1	1
1402.0	0	1	1
1542.0	0	1	1
1620.0	0	1	1
1711.0	0	1	1
1899.0	0	1	1
2035.0	0	1	1