## 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-DMSO_4.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-DMSO_4.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-DMSO_4.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 09:57:44 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	2010	50627257	45646266	0	1793	10532552	0	0.208055	104139597

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	35432660	35432660
2.0	1.614991	3402859	3402859
3.0	1.993204	631233	631233
4.0	2.225802	213303	213303
5.0	2.368848	107475	107475
6.0	2.45682	66177	66177
7.0	2.510921	44540	44540
8.0	2.544194	32347	32347
9.0	2.564656	24298	24298
10.0	2.57724	18662	18662
11.0	2.584979	14786	14786
12.0	2.589738	12071	12071
13.0	2.592665	9775	9775
14.0	2.594465	8253	8253
15.0	2.595572	7000	7000
16.0	2.596253	5990	5990
17.0	2.596672	5207	5207
18.0	2.596929	4556	4556
19.0	2.597087	3967	3967
20.0	2.597185	3455	3455
21.0	2.597245	3096	3096
22.0	2.597282	2744	2744
23.0	2.597304	2417	2417
24.0	2.597318	2241	2241
25.0	2.597327	2002	2002
26.0	2.597332	1864	1864
27.0	2.597335	1689	1689
28.0	2.597337	1552	1552
29.0	2.597338	1466	1466
30.0	2.597339	1309	1309
31.0	2.59734	1192	1192
32.0	2.59734	1117	1117
33.0	2.59734	1004	1004
34.0	2.59734	869	869
35.0	2.59734	870	870
36.0	2.59734	809	809
37.0	2.59734	770	770
38.0	2.59734	692	692
39.0	2.59734	638	638
40.0	2.59734	657	657
41.0	2.59734	580	580
42.0	2.59734	604	604
43.0	2.59734	543	543
44.0	2.59734	516	516
45.0	2.59734	463	463
46.0	2.59734	419	419
47.0	2.59734	439	439
48.0	2.59734	406	406
49.0	2.59734	393	393
50.0	2.59734	348	348
51.0	2.59734	347	347
52.0	2.59734	324	324
53.0	2.59734	313	313
54.0	2.59734	329	329
55.0	2.59734	300	300
56.0	2.59734	279	279
57.0	2.59734	268	268
58.0	2.59734	241	241
59.0	2.59734	237	237
60.0	2.59734	242	242
61.0	2.59734	216	216
62.0	2.59734	223	223
63.0	2.59734	201	201
64.0	2.59734	198	198
65.0	2.59734	210	210
66.0	2.59734	195	195
67.0	2.59734	178	178
68.0	2.59734	173	173
69.0	2.59734	149	149
70.0	2.59734	169	169
71.0	2.59734	167	167
72.0	2.59734	166	166
73.0	2.59734	137	137
74.0	2.59734	121	121
75.0	2.59734	144	144
76.0	2.59734	128	128
77.0	2.59734	121	121
78.0	2.59734	129	129
79.0	2.59734	126	126
80.0	2.59734	116	116
81.0	2.59734	114	114
82.0	2.59734	106	106
83.0	2.59734	117	117
84.0	2.59734	91	91
85.0	2.59734	83	83
86.0	2.59734	102	102
87.0	2.59734	113	113
88.0	2.59734	80	80
89.0	2.59734	89	89
90.0	2.59734	89	89
91.0	2.59734	83	83
92.0	2.59734	55	55
93.0	2.59734	97	97
94.0	2.59734	80	80
95.0	2.59734	78	78
96.0	2.59734	74	74
97.0	2.59734	81	81
98.0	2.59734	71	71
99.0	2.59734	75	75
100.0	2.59734	64	64
101.0	0	82	82
102.0	0	63	63
103.0	0	65	65
104.0	0	62	62
105.0	0	58	58
106.0	0	54	54
107.0	0	55	55
108.0	0	53	53
109.0	0	39	39
110.0	0	50	50
111.0	0	46	46
112.0	0	52	52
113.0	0	49	49
114.0	0	47	47
115.0	0	53	53
116.0	0	42	42
117.0	0	45	45
118.0	0	33	33
119.0	0	37	37
120.0	0	48	48
121.0	0	38	38
122.0	0	38	38
123.0	0	43	43
124.0	0	36	36
125.0	0	32	32
126.0	0	38	38
127.0	0	45	45
128.0	0	40	40
129.0	0	40	40
130.0	0	39	39
131.0	0	40	40
132.0	0	26	26
133.0	0	30	30
134.0	0	33	33
135.0	0	34	34
136.0	0	23	23
137.0	0	26	26
138.0	0	30	30
139.0	0	31	31
140.0	0	33	33
141.0	0	37	37
142.0	0	27	27
143.0	0	28	28
144.0	0	24	24
145.0	0	24	24
146.0	0	18	18
147.0	0	28	28
148.0	0	22	22
149.0	0	26	26
150.0	0	24	24
151.0	0	23	23
152.0	0	22	22
153.0	0	15	15
154.0	0	26	26
155.0	0	29	29
156.0	0	25	25
157.0	0	21	21
158.0	0	20	20
159.0	0	22	22
160.0	0	16	16
161.0	0	24	24
162.0	0	21	21
163.0	0	21	21
164.0	0	21	21
165.0	0	17	17
166.0	0	16	16
167.0	0	22	22
168.0	0	18	18
169.0	0	18	18
170.0	0	12	12
171.0	0	24	24
172.0	0	11	11
173.0	0	15	15
174.0	0	18	18
175.0	0	18	18
176.0	0	20	20
177.0	0	18	18
178.0	0	16	16
179.0	0	14	14
180.0	0	11	11
181.0	0	15	15
182.0	0	14	14
183.0	0	23	23
184.0	0	12	12
185.0	0	17	17
186.0	0	10	10
187.0	0	8	8
188.0	0	11	11
189.0	0	11	11
190.0	0	10	10
191.0	0	26	26
192.0	0	8	8
193.0	0	22	22
194.0	0	10	10
195.0	0	14	14
196.0	0	13	13
197.0	0	13	13
198.0	0	16	16
199.0	0	11	11
200.0	0	5	5
201.0	0	11	11
202.0	0	7	7
203.0	0	14	14
204.0	0	14	14
205.0	0	12	12
206.0	0	5	5
207.0	0	9	9
208.0	0	7	7
209.0	0	14	14
210.0	0	20	20
211.0	0	11	11
212.0	0	11	11
213.0	0	16	16
214.0	0	6	6
215.0	0	8	8
216.0	0	13	13
217.0	0	4	4
218.0	0	11	11
219.0	0	10	10
220.0	0	8	8
221.0	0	11	11
222.0	0	9	9
223.0	0	11	11
224.0	0	11	11
225.0	0	10	10
226.0	0	10	10
227.0	0	10	10
228.0	0	11	11
229.0	0	8	8
230.0	0	9	9
231.0	0	7	7
232.0	0	5	5
233.0	0	10	10
234.0	0	13	13
235.0	0	8	8
236.0	0	6	6
237.0	0	3	3
238.0	0	7	7
239.0	0	5	5
240.0	0	5	5
241.0	0	8	8
242.0	0	10	10
243.0	0	5	5
244.0	0	7	7
245.0	0	8	8
246.0	0	7	7
247.0	0	6	6
248.0	0	12	12
249.0	0	9	9
250.0	0	14	14
251.0	0	10	10
252.0	0	7	7
253.0	0	9	9
254.0	0	8	8
255.0	0	5	5
256.0	0	5	5
257.0	0	9	9
258.0	0	3	3
259.0	0	7	7
260.0	0	15	15
261.0	0	10	10
262.0	0	6	6
263.0	0	5	5
264.0	0	8	8
265.0	0	4	4
266.0	0	3	3
267.0	0	5	5
268.0	0	8	8
269.0	0	4	4
270.0	0	4	4
271.0	0	8	8
272.0	0	7	7
273.0	0	6	6
274.0	0	7	7
275.0	0	7	7
276.0	0	6	6
277.0	0	8	8
278.0	0	4	4
279.0	0	3	3
280.0	0	8	8
281.0	0	4	4
282.0	0	7	7
283.0	0	5	5
284.0	0	6	6
285.0	0	7	7
286.0	0	5	5
287.0	0	5	5
288.0	0	4	4
289.0	0	3	3
290.0	0	6	6
291.0	0	6	6
292.0	0	5	5
293.0	0	5	5
294.0	0	2	2
295.0	0	7	7
296.0	0	8	8
297.0	0	4	4
298.0	0	3	3
299.0	0	5	5
300.0	0	6	6
301.0	0	5	5
302.0	0	7	7
303.0	0	9	9
304.0	0	7	7
305.0	0	4	4
306.0	0	8	8
307.0	0	5	5
308.0	0	5	5
309.0	0	8	8
310.0	0	6	6
311.0	0	2	2
312.0	0	3	3
313.0	0	6	6
314.0	0	3	3
315.0	0	3	3
316.0	0	5	5
317.0	0	3	3
318.0	0	2	2
319.0	0	4	4
320.0	0	6	6
321.0	0	5	5
322.0	0	4	4
323.0	0	6	6
324.0	0	7	7
325.0	0	6	6
326.0	0	3	3
327.0	0	4	4
328.0	0	2	2
329.0	0	5	5
330.0	0	6	6
331.0	0	3	3
332.0	0	5	5
333.0	0	5	5
334.0	0	1	1
335.0	0	3	3
336.0	0	2	2
337.0	0	4	4
338.0	0	4	4
339.0	0	2	2
340.0	0	2	2
341.0	0	5	5
342.0	0	7	7
343.0	0	2	2
344.0	0	5	5
345.0	0	5	5
346.0	0	3	3
347.0	0	4	4
348.0	0	9	9
349.0	0	3	3
350.0	0	1	1
351.0	0	5	5
352.0	0	1	1
353.0	0	8	8
354.0	0	2	2
355.0	0	4	4
356.0	0	5	5
357.0	0	4	4
358.0	0	5	5
359.0	0	3	3
360.0	0	6	6
361.0	0	2	2
362.0	0	3	3
363.0	0	4	4
364.0	0	2	2
365.0	0	2	2
366.0	0	1	1
367.0	0	1	1
368.0	0	2	2
369.0	0	3	3
370.0	0	4	4
371.0	0	5	5
372.0	0	4	4
373.0	0	2	2
374.0	0	4	4
375.0	0	3	3
377.0	0	4	4
378.0	0	5	5
379.0	0	3	3
380.0	0	3	3
381.0	0	3	3
382.0	0	1	1
383.0	0	2	2
384.0	0	2	2
385.0	0	1	1
386.0	0	2	2
387.0	0	2	2
388.0	0	5	5
389.0	0	1	1
390.0	0	3	3
391.0	0	2	2
392.0	0	1	1
393.0	0	3	3
394.0	0	3	3
395.0	0	3	3
397.0	0	2	2
398.0	0	3	3
399.0	0	3	3
400.0	0	2	2
401.0	0	5	5
402.0	0	3	3
403.0	0	7	7
404.0	0	2	2
405.0	0	3	3
406.0	0	1	1
407.0	0	1	1
408.0	0	4	4
409.0	0	4	4
410.0	0	1	1
411.0	0	3	3
412.0	0	5	5
413.0	0	5	5
414.0	0	2	2
415.0	0	1	1
416.0	0	1	1
417.0	0	1	1
419.0	0	2	2
420.0	0	5	5
421.0	0	6	6
422.0	0	3	3
423.0	0	1	1
424.0	0	2	2
425.0	0	2	2
426.0	0	6	6
427.0	0	3	3
428.0	0	5	5
430.0	0	4	4
431.0	0	2	2
433.0	0	1	1
434.0	0	2	2
436.0	0	3	3
437.0	0	2	2
438.0	0	3	3
439.0	0	3	3
441.0	0	1	1
442.0	0	1	1
443.0	0	2	2
446.0	0	1	1
447.0	0	2	2
448.0	0	4	4
449.0	0	1	1
450.0	0	1	1
452.0	0	2	2
453.0	0	3	3
455.0	0	3	3
456.0	0	2	2
457.0	0	2	2
459.0	0	2	2
460.0	0	2	2
461.0	0	2	2
463.0	0	2	2
464.0	0	1	1
465.0	0	1	1
466.0	0	2	2
468.0	0	2	2
469.0	0	2	2
470.0	0	4	4
471.0	0	2	2
473.0	0	2	2
474.0	0	3	3
475.0	0	1	1
476.0	0	2	2
477.0	0	1	1
478.0	0	2	2
479.0	0	1	1
480.0	0	1	1
484.0	0	2	2
485.0	0	3	3
486.0	0	2	2
487.0	0	5	5
488.0	0	2	2
489.0	0	1	1
492.0	0	3	3
493.0	0	1	1
494.0	0	1	1
497.0	0	1	1
498.0	0	1	1
499.0	0	3	3
501.0	0	2	2
502.0	0	2	2
504.0	0	2	2
505.0	0	1	1
507.0	0	1	1
508.0	0	1	1
509.0	0	1	1
510.0	0	3	3
512.0	0	2	2
513.0	0	1	1
514.0	0	1	1
515.0	0	1	1
516.0	0	2	2
517.0	0	1	1
518.0	0	1	1
523.0	0	2	2
524.0	0	1	1
525.0	0	3	3
526.0	0	1	1
528.0	0	4	4
529.0	0	1	1
530.0	0	1	1
532.0	0	1	1
534.0	0	2	2
535.0	0	2	2
538.0	0	1	1
539.0	0	2	2
541.0	0	2	2
543.0	0	3	3
544.0	0	2	2
545.0	0	3	3
550.0	0	3	3
551.0	0	3	3
554.0	0	1	1
557.0	0	1	1
558.0	0	2	2
559.0	0	2	2
563.0	0	1	1
564.0	0	1	1
566.0	0	1	1
569.0	0	1	1
572.0	0	1	1
574.0	0	1	1
575.0	0	1	1
577.0	0	2	2
578.0	0	1	1
580.0	0	2	2
583.0	0	2	2
584.0	0	3	3
585.0	0	1	1
589.0	0	1	1
590.0	0	1	1
592.0	0	1	1
593.0	0	2	2
595.0	0	1	1
596.0	0	1	1
597.0	0	1	1
600.0	0	2	2
601.0	0	1	1
604.0	0	1	1
605.0	0	2	2
607.0	0	1	1
609.0	0	1	1
610.0	0	1	1
612.0	0	1	1
614.0	0	2	2
616.0	0	1	1
617.0	0	1	1
618.0	0	2	2
619.0	0	2	2
620.0	0	1	1
621.0	0	1	1
622.0	0	1	1
623.0	0	1	1
625.0	0	1	1
627.0	0	3	3
628.0	0	1	1
629.0	0	1	1
631.0	0	1	1
632.0	0	2	2
633.0	0	1	1
636.0	0	1	1
639.0	0	1	1
640.0	0	1	1
641.0	0	2	2
643.0	0	3	3
645.0	0	1	1
646.0	0	1	1
650.0	0	1	1
651.0	0	1	1
652.0	0	2	2
653.0	0	3	3
654.0	0	2	2
655.0	0	1	1
661.0	0	1	1
665.0	0	1	1
668.0	0	1	1
669.0	0	1	1
671.0	0	1	1
672.0	0	1	1
676.0	0	2	2
677.0	0	1	1
678.0	0	1	1
681.0	0	2	2
682.0	0	1	1
684.0	0	3	3
686.0	0	1	1
687.0	0	2	2
688.0	0	1	1
692.0	0	1	1
694.0	0	1	1
701.0	0	1	1
702.0	0	1	1
703.0	0	1	1
706.0	0	1	1
709.0	0	1	1
710.0	0	1	1
712.0	0	1	1
717.0	0	1	1
719.0	0	1	1
721.0	0	2	2
722.0	0	1	1
725.0	0	2	2
726.0	0	1	1
728.0	0	1	1
729.0	0	1	1
735.0	0	2	2
738.0	0	1	1
741.0	0	1	1
743.0	0	1	1
744.0	0	1	1
749.0	0	1	1
752.0	0	1	1
753.0	0	1	1
755.0	0	1	1
758.0	0	2	2
760.0	0	1	1
767.0	0	1	1
768.0	0	1	1
769.0	0	1	1
772.0	0	1	1
773.0	0	2	2
775.0	0	1	1
782.0	0	1	1
786.0	0	1	1
791.0	0	1	1
800.0	0	1	1
801.0	0	1	1
802.0	0	1	1
808.0	0	1	1
809.0	0	1	1
810.0	0	1	1
815.0	0	1	1
816.0	0	1	1
821.0	0	1	1
825.0	0	1	1
833.0	0	2	2
849.0	0	1	1
851.0	0	1	1
864.0	0	2	2
869.0	0	1	1
874.0	0	1	1
875.0	0	1	1
876.0	0	1	1
878.0	0	1	1
879.0	0	1	1
881.0	0	1	1
883.0	0	2	2
888.0	0	1	1
894.0	0	1	1
898.0	0	2	2
915.0	0	1	1
924.0	0	1	1
927.0	0	1	1
934.0	0	1	1
942.0	0	1	1
944.0	0	1	1
945.0	0	1	1
949.0	0	1	1
951.0	0	1	1
952.0	0	1	1
961.0	0	1	1
966.0	0	1	1
968.0	0	1	1
979.0	0	1	1
980.0	0	1	1
987.0	0	1	1
993.0	0	1	1
996.0	0	1	1
1004.0	0	1	1
1007.0	0	1	1
1008.0	0	1	1
1010.0	0	1	1
1049.0	0	1	1
1059.0	0	1	1
1066.0	0	1	1
1067.0	0	1	1
1072.0	0	2	2
1074.0	0	1	1
1077.0	0	1	1
1108.0	0	1	1
1128.0	0	1	1
1134.0	0	1	1
1143.0	0	1	1
1148.0	0	2	2
1154.0	0	1	1
1155.0	0	1	1
1194.0	0	1	1
1199.0	0	1	1
1200.0	0	1	1
1224.0	0	1	1
1238.0	0	1	1
1255.0	0	1	1
1259.0	0	2	2
1283.0	0	1	1
1330.0	0	1	1
1336.0	0	1	1
1346.0	0	1	1
1347.0	0	1	1
1354.0	0	1	1
1355.0	0	1	1
1356.0	0	1	1
1359.0	0	1	1
1378.0	0	1	1
1417.0	0	1	1
1419.0	0	1	1
1485.0	0	1	1
1519.0	0	1	1
1521.0	0	1	1
1556.0	0	2	2
1574.0	0	1	1
1592.0	0	1	1
1618.0	0	1	1
1635.0	0	1	1
1650.0	0	1	1
1660.0	0	1	1
1661.0	0	1	1
1666.0	0	1	1
1668.0	0	2	2
1730.0	0	1	1
1737.0	0	1	1
1782.0	0	1	1
1828.0	0	1	1
1852.0	0	1	1
1956.0	0	1	1
1961.0	0	1	1
2031.0	0	1	1
2127.0	0	1	1
2134.0	0	1	1
2205.0	0	1	1
2209.0	0	1	1
2230.0	0	1	1
2294.0	0	1	1
2308.0	0	1	1
2337.0	0	1	1
2358.0	0	1	1
2372.0	0	1	1
2381.0	0	1	1
2385.0	0	1	1
2470.0	0	1	1
2490.0	0	1	1
2572.0	0	1	1
2707.0	0	1	1
2719.0	0	1	1
2730.0	0	1	1
2778.0	0	1	1
2860.0	0	1	1
3223.0	0	1	1
3293.0	0	1	1
5827.0	0	1	1
7995.0	0	1	1