## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-TA100nM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-TA100nM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-TA100nM_2.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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Oct 04 10:14:00 CEST 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
Unknown Library	2375	47129845	47426778	0	2204	10237597	0	0.217239	92127595

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32759231	32759231
2.0	1.599553	2968068	2968068
3.0	1.959016	531331	531331
4.0	2.174533	201986	201986
5.0	2.303747	109085	109085
6.0	2.381218	68165	68165
7.0	2.427666	46860	46860
8.0	2.455513	33766	33766
9.0	2.47221	25120	25120
10.0	2.48222	19606	19606
11.0	2.488222	15437	15437
12.0	2.49182	12573	12573
13.0	2.493977	10505	10505
14.0	2.495271	8753	8753
15.0	2.496046	7326	7326
16.0	2.496511	6218	6218
17.0	2.49679	5409	5409
18.0	2.496957	4677	4677
19.0	2.497057	4193	4193
20.0	2.497117	3686	3686
21.0	2.497153	3248	3248
22.0	2.497175	2963	2963
23.0	2.497188	2562	2562
24.0	2.497196	2468	2468
25.0	2.4972	2080	2080
26.0	2.497203	1914	1914
27.0	2.497205	1765	1765
28.0	2.497206	1716	1716
29.0	2.497207	1535	1535
30.0	2.497207	1421	1421
31.0	2.497207	1307	1307
32.0	2.497207	1162	1162
33.0	2.497207	1107	1107
34.0	2.497207	994	994
35.0	2.497207	1008	1008
36.0	2.497207	918	918
37.0	2.497207	810	810
38.0	2.497207	786	786
39.0	2.497207	761	761
40.0	2.497207	744	744
41.0	2.497207	642	642
42.0	2.497207	638	638
43.0	2.497207	587	587
44.0	2.497207	545	545
45.0	2.497207	552	552
46.0	2.497207	484	484
47.0	2.497207	491	491
48.0	2.497207	447	447
49.0	2.497207	423	423
50.0	2.497207	445	445
51.0	2.497207	378	378
52.0	2.497207	367	367
53.0	2.497207	343	343
54.0	2.497207	334	334
55.0	2.497207	331	331
56.0	2.497207	311	311
57.0	2.497207	287	287
58.0	2.497207	287	287
59.0	2.497207	277	277
60.0	2.497207	284	284
61.0	2.497207	261	261
62.0	2.497207	262	262
63.0	2.497207	247	247
64.0	2.497207	266	266
65.0	2.497207	208	208
66.0	2.497207	189	189
67.0	2.497207	175	175
68.0	2.497207	192	192
69.0	2.497207	191	191
70.0	2.497207	164	164
71.0	2.497207	195	195
72.0	2.497207	192	192
73.0	2.497207	166	166
74.0	2.497207	171	171
75.0	2.497207	150	150
76.0	2.497207	134	134
77.0	2.497207	147	147
78.0	2.497207	129	129
79.0	2.497207	118	118
80.0	2.497207	121	121
81.0	2.497207	127	127
82.0	2.497207	129	129
83.0	2.497207	119	119
84.0	2.497207	115	115
85.0	2.497207	113	113
86.0	2.497207	114	114
87.0	2.497207	91	91
88.0	2.497207	108	108
89.0	2.497207	88	88
90.0	2.497207	97	97
91.0	2.497207	88	88
92.0	2.497207	82	82
93.0	2.497207	78	78
94.0	2.497207	85	85
95.0	2.497207	89	89
96.0	2.497207	80	80
97.0	2.497207	74	74
98.0	2.497207	72	72
99.0	2.497207	71	71
100.0	2.497207	87	87
101.0	0	80	80
102.0	0	61	61
103.0	0	71	71
104.0	0	61	61
105.0	0	77	77
106.0	0	53	53
107.0	0	56	56
108.0	0	62	62
109.0	0	48	48
110.0	0	54	54
111.0	0	48	48
112.0	0	52	52
113.0	0	55	55
114.0	0	53	53
115.0	0	54	54
116.0	0	71	71
117.0	0	56	56
118.0	0	51	51
119.0	0	53	53
120.0	0	46	46
121.0	0	40	40
122.0	0	40	40
123.0	0	39	39
124.0	0	47	47
125.0	0	43	43
126.0	0	38	38
127.0	0	40	40
128.0	0	37	37
129.0	0	40	40
130.0	0	45	45
131.0	0	45	45
132.0	0	42	42
133.0	0	38	38
134.0	0	33	33
135.0	0	34	34
136.0	0	44	44
137.0	0	33	33
138.0	0	34	34
139.0	0	25	25
140.0	0	27	27
141.0	0	26	26
142.0	0	39	39
143.0	0	33	33
144.0	0	32	32
145.0	0	33	33
146.0	0	29	29
147.0	0	25	25
148.0	0	35	35
149.0	0	33	33
150.0	0	32	32
151.0	0	15	15
152.0	0	20	20
153.0	0	19	19
154.0	0	19	19
155.0	0	27	27
156.0	0	21	21
157.0	0	27	27
158.0	0	28	28
159.0	0	29	29
160.0	0	21	21
161.0	0	19	19
162.0	0	27	27
163.0	0	28	28
164.0	0	13	13
165.0	0	22	22
166.0	0	20	20
167.0	0	26	26
168.0	0	22	22
169.0	0	15	15
170.0	0	16	16
171.0	0	15	15
172.0	0	23	23
173.0	0	22	22
174.0	0	15	15
175.0	0	17	17
176.0	0	19	19
177.0	0	14	14
178.0	0	13	13
179.0	0	26	26
180.0	0	20	20
181.0	0	23	23
182.0	0	19	19
183.0	0	14	14
184.0	0	13	13
185.0	0	18	18
186.0	0	14	14
187.0	0	20	20
188.0	0	22	22
189.0	0	12	12
190.0	0	17	17
191.0	0	14	14
192.0	0	5	5
193.0	0	10	10
194.0	0	13	13
195.0	0	12	12
196.0	0	19	19
197.0	0	10	10
198.0	0	20	20
199.0	0	10	10
200.0	0	12	12
201.0	0	14	14
202.0	0	11	11
203.0	0	13	13
204.0	0	15	15
205.0	0	9	9
206.0	0	18	18
207.0	0	13	13
208.0	0	20	20
209.0	0	13	13
210.0	0	10	10
211.0	0	8	8
212.0	0	18	18
213.0	0	8	8
214.0	0	6	6
215.0	0	14	14
216.0	0	10	10
217.0	0	10	10
218.0	0	19	19
219.0	0	10	10
220.0	0	20	20
221.0	0	16	16
222.0	0	10	10
223.0	0	13	13
224.0	0	17	17
225.0	0	12	12
226.0	0	9	9
227.0	0	11	11
228.0	0	8	8
229.0	0	14	14
230.0	0	8	8
231.0	0	8	8
232.0	0	8	8
233.0	0	11	11
234.0	0	10	10
235.0	0	8	8
236.0	0	9	9
237.0	0	9	9
238.0	0	12	12
239.0	0	10	10
240.0	0	15	15
241.0	0	8	8
242.0	0	8	8
243.0	0	2	2
244.0	0	4	4
245.0	0	5	5
246.0	0	7	7
247.0	0	8	8
248.0	0	8	8
249.0	0	10	10
250.0	0	9	9
251.0	0	8	8
252.0	0	5	5
253.0	0	8	8
254.0	0	7	7
255.0	0	12	12
256.0	0	7	7
257.0	0	9	9
258.0	0	13	13
259.0	0	9	9
260.0	0	9	9
261.0	0	8	8
262.0	0	6	6
263.0	0	9	9
264.0	0	7	7
265.0	0	4	4
266.0	0	6	6
267.0	0	4	4
268.0	0	13	13
269.0	0	2	2
270.0	0	12	12
271.0	0	2	2
272.0	0	15	15
273.0	0	8	8
274.0	0	8	8
275.0	0	7	7
276.0	0	6	6
277.0	0	6	6
278.0	0	5	5
279.0	0	10	10
280.0	0	6	6
282.0	0	5	5
283.0	0	6	6
284.0	0	6	6
285.0	0	8	8
286.0	0	3	3
287.0	0	3	3
288.0	0	9	9
289.0	0	2	2
290.0	0	3	3
291.0	0	7	7
292.0	0	5	5
293.0	0	9	9
294.0	0	4	4
295.0	0	5	5
296.0	0	7	7
297.0	0	5	5
298.0	0	3	3
299.0	0	1	1
300.0	0	2	2
301.0	0	5	5
302.0	0	4	4
303.0	0	2	2
304.0	0	4	4
305.0	0	4	4
306.0	0	3	3
307.0	0	4	4
308.0	0	5	5
310.0	0	3	3
311.0	0	6	6
312.0	0	6	6
313.0	0	3	3
314.0	0	7	7
315.0	0	7	7
316.0	0	5	5
317.0	0	7	7
318.0	0	2	2
319.0	0	4	4
320.0	0	3	3
321.0	0	4	4
322.0	0	7	7
323.0	0	3	3
324.0	0	2	2
325.0	0	5	5
326.0	0	6	6
327.0	0	4	4
328.0	0	1	1
329.0	0	5	5
330.0	0	6	6
331.0	0	3	3
332.0	0	3	3
333.0	0	4	4
334.0	0	5	5
335.0	0	3	3
336.0	0	2	2
337.0	0	3	3
338.0	0	4	4
339.0	0	5	5
340.0	0	3	3
341.0	0	2	2
342.0	0	3	3
343.0	0	2	2
344.0	0	1	1
345.0	0	3	3
346.0	0	1	1
347.0	0	6	6
348.0	0	2	2
349.0	0	1	1
350.0	0	6	6
351.0	0	3	3
352.0	0	9	9
353.0	0	7	7
354.0	0	6	6
355.0	0	4	4
356.0	0	2	2
357.0	0	1	1
358.0	0	5	5
359.0	0	1	1
360.0	0	2	2
361.0	0	4	4
362.0	0	5	5
363.0	0	4	4
365.0	0	6	6
366.0	0	4	4
367.0	0	5	5
368.0	0	4	4
369.0	0	1	1
370.0	0	2	2
371.0	0	3	3
372.0	0	6	6
373.0	0	3	3
374.0	0	6	6
375.0	0	3	3
376.0	0	4	4
377.0	0	1	1
378.0	0	2	2
379.0	0	3	3
380.0	0	1	1
381.0	0	3	3
382.0	0	4	4
383.0	0	3	3
384.0	0	4	4
385.0	0	3	3
386.0	0	1	1
387.0	0	3	3
388.0	0	1	1
389.0	0	1	1
390.0	0	3	3
391.0	0	3	3
392.0	0	2	2
393.0	0	6	6
394.0	0	3	3
395.0	0	3	3
396.0	0	3	3
397.0	0	5	5
399.0	0	3	3
400.0	0	4	4
401.0	0	1	1
402.0	0	4	4
403.0	0	4	4
404.0	0	6	6
405.0	0	2	2
407.0	0	3	3
408.0	0	3	3
409.0	0	3	3
410.0	0	2	2
411.0	0	6	6
413.0	0	4	4
414.0	0	1	1
415.0	0	1	1
417.0	0	3	3
418.0	0	4	4
419.0	0	1	1
420.0	0	3	3
421.0	0	2	2
422.0	0	1	1
423.0	0	3	3
424.0	0	3	3
425.0	0	3	3
426.0	0	2	2
427.0	0	6	6
428.0	0	1	1
429.0	0	2	2
430.0	0	1	1
431.0	0	2	2
432.0	0	2	2
433.0	0	4	4
435.0	0	2	2
436.0	0	4	4
437.0	0	3	3
438.0	0	3	3
439.0	0	5	5
440.0	0	1	1
441.0	0	2	2
444.0	0	2	2
445.0	0	1	1
446.0	0	4	4
447.0	0	1	1
448.0	0	3	3
449.0	0	2	2
450.0	0	2	2
452.0	0	3	3
453.0	0	1	1
454.0	0	1	1
455.0	0	1	1
456.0	0	2	2
457.0	0	2	2
458.0	0	3	3
459.0	0	1	1
460.0	0	1	1
461.0	0	2	2
462.0	0	3	3
463.0	0	3	3
465.0	0	1	1
466.0	0	1	1
467.0	0	1	1
468.0	0	1	1
469.0	0	1	1
471.0	0	1	1
472.0	0	2	2
473.0	0	1	1
475.0	0	3	3
476.0	0	2	2
477.0	0	1	1
478.0	0	3	3
480.0	0	3	3
483.0	0	2	2
484.0	0	1	1
485.0	0	3	3
487.0	0	1	1
488.0	0	3	3
490.0	0	1	1
491.0	0	1	1
492.0	0	4	4
493.0	0	1	1
494.0	0	1	1
495.0	0	1	1
496.0	0	1	1
497.0	0	3	3
498.0	0	2	2
499.0	0	2	2
501.0	0	2	2
503.0	0	1	1
504.0	0	1	1
505.0	0	3	3
506.0	0	2	2
507.0	0	2	2
509.0	0	2	2
512.0	0	5	5
514.0	0	1	1
516.0	0	2	2
518.0	0	2	2
519.0	0	1	1
520.0	0	1	1
522.0	0	3	3
523.0	0	1	1
524.0	0	1	1
525.0	0	1	1
527.0	0	1	1
528.0	0	2	2
529.0	0	1	1
532.0	0	2	2
533.0	0	1	1
535.0	0	2	2
539.0	0	1	1
540.0	0	1	1
541.0	0	3	3
543.0	0	1	1
544.0	0	1	1
545.0	0	1	1
547.0	0	1	1
548.0	0	2	2
549.0	0	1	1
551.0	0	5	5
552.0	0	2	2
553.0	0	3	3
554.0	0	2	2
555.0	0	1	1
556.0	0	2	2
558.0	0	7	7
559.0	0	2	2
560.0	0	2	2
561.0	0	4	4
563.0	0	2	2
564.0	0	1	1
566.0	0	1	1
567.0	0	2	2
569.0	0	2	2
571.0	0	2	2
573.0	0	1	1
576.0	0	1	1
578.0	0	2	2
582.0	0	1	1
583.0	0	1	1
584.0	0	1	1
585.0	0	1	1
587.0	0	1	1
589.0	0	1	1
590.0	0	1	1
591.0	0	1	1
592.0	0	1	1
598.0	0	1	1
600.0	0	1	1
601.0	0	1	1
603.0	0	1	1
605.0	0	1	1
607.0	0	2	2
611.0	0	2	2
612.0	0	3	3
613.0	0	1	1
614.0	0	1	1
620.0	0	1	1
623.0	0	2	2
625.0	0	2	2
628.0	0	1	1
633.0	0	1	1
635.0	0	1	1
637.0	0	1	1
638.0	0	2	2
639.0	0	1	1
640.0	0	1	1
641.0	0	1	1
642.0	0	3	3
643.0	0	1	1
645.0	0	2	2
646.0	0	1	1
647.0	0	1	1
652.0	0	1	1
653.0	0	1	1
654.0	0	1	1
655.0	0	2	2
657.0	0	1	1
658.0	0	1	1
660.0	0	1	1
661.0	0	1	1
662.0	0	2	2
664.0	0	1	1
666.0	0	1	1
667.0	0	2	2
671.0	0	1	1
677.0	0	1	1
678.0	0	1	1
679.0	0	3	3
681.0	0	1	1
684.0	0	1	1
686.0	0	1	1
690.0	0	1	1
693.0	0	1	1
694.0	0	1	1
697.0	0	1	1
700.0	0	1	1
704.0	0	1	1
706.0	0	1	1
708.0	0	1	1
710.0	0	2	2
711.0	0	1	1
712.0	0	2	2
718.0	0	1	1
719.0	0	3	3
722.0	0	1	1
728.0	0	1	1
730.0	0	2	2
732.0	0	2	2
741.0	0	2	2
744.0	0	1	1
748.0	0	1	1
752.0	0	1	1
755.0	0	1	1
756.0	0	1	1
758.0	0	1	1
759.0	0	1	1
761.0	0	1	1
762.0	0	1	1
766.0	0	1	1
772.0	0	1	1
779.0	0	1	1
785.0	0	1	1
791.0	0	1	1
800.0	0	3	3
801.0	0	1	1
803.0	0	1	1
805.0	0	1	1
807.0	0	2	2
808.0	0	1	1
812.0	0	1	1
818.0	0	1	1
822.0	0	1	1
823.0	0	1	1
826.0	0	1	1
830.0	0	2	2
831.0	0	2	2
834.0	0	1	1
836.0	0	1	1
840.0	0	1	1
842.0	0	1	1
846.0	0	2	2
848.0	0	1	1
852.0	0	1	1
855.0	0	1	1
857.0	0	2	2
867.0	0	2	2
869.0	0	1	1
870.0	0	1	1
880.0	0	1	1
882.0	0	2	2
884.0	0	1	1
886.0	0	1	1
887.0	0	1	1
890.0	0	1	1
894.0	0	1	1
901.0	0	1	1
902.0	0	1	1
905.0	0	1	1
912.0	0	1	1
919.0	0	1	1
921.0	0	1	1
923.0	0	1	1
924.0	0	1	1
931.0	0	1	1
936.0	0	1	1
937.0	0	1	1
938.0	0	2	2
942.0	0	1	1
943.0	0	2	2
947.0	0	2	2
956.0	0	1	1
959.0	0	1	1
964.0	0	1	1
987.0	0	2	2
990.0	0	2	2
991.0	0	1	1
1009.0	0	1	1
1011.0	0	1	1
1025.0	0	2	2
1035.0	0	1	1
1040.0	0	1	1
1042.0	0	1	1
1044.0	0	1	1
1050.0	0	1	1
1051.0	0	1	1
1057.0	0	2	2
1067.0	0	1	1
1068.0	0	1	1
1072.0	0	1	1
1080.0	0	1	1
1093.0	0	1	1
1104.0	0	1	1
1105.0	0	1	1
1121.0	0	1	1
1130.0	0	1	1
1139.0	0	1	1
1146.0	0	1	1
1147.0	0	1	1
1159.0	0	1	1
1164.0	0	1	1
1178.0	0	1	1
1193.0	0	1	1
1194.0	0	1	1
1200.0	0	1	1
1212.0	0	1	1
1243.0	0	2	2
1250.0	0	1	1
1258.0	0	1	1
1267.0	0	1	1
1295.0	0	1	1
1329.0	0	1	1
1330.0	0	1	1
1332.0	0	1	1
1338.0	0	2	2
1382.0	0	1	1
1402.0	0	1	1
1408.0	0	1	1
1409.0	0	1	1
1420.0	0	1	1
1426.0	0	1	1
1429.0	0	1	1
1443.0	0	1	1
1445.0	0	1	1
1495.0	0	1	1
1499.0	0	1	1
1502.0	0	1	1
1512.0	0	1	1
1537.0	0	1	1
1552.0	0	1	1
1568.0	0	1	1
1617.0	0	1	1
1652.0	0	1	1
1667.0	0	1	1
1672.0	0	1	1
1674.0	0	1	1
1725.0	0	1	1
1731.0	0	1	1
1732.0	0	1	1
1734.0	0	1	1
1776.0	0	1	1
1798.0	0	1	1
1871.0	0	1	1
1898.0	0	1	1
1916.0	0	1	1
1919.0	0	1	1
1923.0	0	1	1
1937.0	0	1	1
1946.0	0	1	1
1988.0	0	1	1
2074.0	0	1	1
2083.0	0	1	1
2168.0	0	1	1
2247.0	0	1	1
2270.0	0	1	1
2427.0	0	1	1
2462.0	0	1	1
2473.0	0	1	1
2542.0	0	1	1
2592.0	0	1	1
2794.0	0	1	1
2950.0	0	1	1
2985.0	0	1	1
3062.0	0	1	1
3100.0	0	1	1
3120.0	0	1	1
3133.0	0	1	1
3188.0	0	1	1
3218.0	0	1	1
3618.0	0	1	1
4038.0	0	1	1
4133.0	0	1	1
4271.0	0	1	1
4531.0	0	1	1
5153.0	0	1	1
6548.0	0	1	1
8501.0	0	1	1