## 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_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-TA100nM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-TA100nM_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 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 10:50:37 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	1432	35620105	31677645	0	1286	8224284	0	0.230902	64739920

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23596970	23596970
2.0	1.576833	2856491	2856491
3.0	1.909569	475350	475350
4.0	2.101501	154092	154092
5.0	2.212215	79739	79739
6.0	2.276078	49636	49636
7.0	2.312916	33839	33839
8.0	2.334165	24239	24239
9.0	2.346423	18013	18013
10.0	2.353493	14031	14031
11.0	2.357572	11469	11469
12.0	2.359924	9270	9270
13.0	2.361281	7404	7404
14.0	2.362064	6326	6326
15.0	2.362516	5387	5387
16.0	2.362776	4637	4637
17.0	2.362926	3980	3980
18.0	2.363013	3410	3410
19.0	2.363063	3032	3032
20.0	2.363092	2568	2568
21.0	2.363109	2404	2404
22.0	2.363118	2162	2162
23.0	2.363124	1998	1998
24.0	2.363127	1719	1719
25.0	2.363129	1555	1555
26.0	2.36313	1429	1429
27.0	2.36313	1282	1282
28.0	2.363131	1134	1134
29.0	2.363131	1085	1085
30.0	2.363131	985	985
31.0	2.363131	919	919
32.0	2.363131	874	874
33.0	2.363131	840	840
34.0	2.363131	741	741
35.0	2.363131	651	651
36.0	2.363131	670	670
37.0	2.363131	573	573
38.0	2.363131	585	585
39.0	2.363131	553	553
40.0	2.363131	554	554
41.0	2.363131	454	454
42.0	2.363131	428	428
43.0	2.363131	385	385
44.0	2.363131	399	399
45.0	2.363131	335	335
46.0	2.363131	347	347
47.0	2.363131	351	351
48.0	2.363131	340	340
49.0	2.363131	287	287
50.0	2.363131	287	287
51.0	2.363131	265	265
52.0	2.363131	270	270
53.0	2.363131	245	245
54.0	2.363131	236	236
55.0	2.363131	192	192
56.0	2.363131	217	217
57.0	2.363131	225	225
58.0	2.363131	227	227
59.0	2.363131	206	206
60.0	2.363131	160	160
61.0	2.363131	164	164
62.0	2.363131	182	182
63.0	2.363131	147	147
64.0	2.363131	157	157
65.0	2.363131	151	151
66.0	2.363131	160	160
67.0	2.363131	151	151
68.0	2.363131	144	144
69.0	2.363131	140	140
70.0	2.363131	125	125
71.0	2.363131	121	121
72.0	2.363131	132	132
73.0	2.363131	112	112
74.0	2.363131	100	100
75.0	2.363131	116	116
76.0	2.363131	114	114
77.0	2.363131	95	95
78.0	2.363131	67	67
79.0	2.363131	94	94
80.0	2.363131	89	89
81.0	2.363131	98	98
82.0	2.363131	86	86
83.0	2.363131	96	96
84.0	2.363131	78	78
85.0	2.363131	85	85
86.0	2.363131	77	77
87.0	2.363131	73	73
88.0	2.363131	68	68
89.0	2.363131	61	61
90.0	2.363131	63	63
91.0	2.363131	66	66
92.0	2.363131	63	63
93.0	2.363131	62	62
94.0	2.363131	54	54
95.0	2.363131	57	57
96.0	2.363131	54	54
97.0	2.363131	62	62
98.0	2.363131	46	46
99.0	2.363131	61	61
100.0	2.363131	52	52
101.0	0	42	42
102.0	0	43	43
103.0	0	43	43
104.0	0	57	57
105.0	0	51	51
106.0	0	42	42
107.0	0	37	37
108.0	0	56	56
109.0	0	52	52
110.0	0	29	29
111.0	0	38	38
112.0	0	35	35
113.0	0	36	36
114.0	0	45	45
115.0	0	36	36
116.0	0	38	38
117.0	0	35	35
118.0	0	39	39
119.0	0	37	37
120.0	0	44	44
121.0	0	27	27
122.0	0	26	26
123.0	0	26	26
124.0	0	25	25
125.0	0	26	26
126.0	0	37	37
127.0	0	34	34
128.0	0	28	28
129.0	0	20	20
130.0	0	34	34
131.0	0	28	28
132.0	0	28	28
133.0	0	20	20
134.0	0	29	29
135.0	0	18	18
136.0	0	29	29
137.0	0	26	26
138.0	0	38	38
139.0	0	12	12
140.0	0	29	29
141.0	0	17	17
142.0	0	16	16
143.0	0	20	20
144.0	0	19	19
145.0	0	20	20
146.0	0	21	21
147.0	0	22	22
148.0	0	17	17
149.0	0	18	18
150.0	0	20	20
151.0	0	21	21
152.0	0	22	22
153.0	0	21	21
154.0	0	15	15
155.0	0	13	13
156.0	0	11	11
157.0	0	21	21
158.0	0	15	15
159.0	0	15	15
160.0	0	19	19
161.0	0	16	16
162.0	0	21	21
163.0	0	16	16
164.0	0	20	20
165.0	0	15	15
166.0	0	12	12
167.0	0	17	17
168.0	0	14	14
169.0	0	14	14
170.0	0	8	8
171.0	0	10	10
172.0	0	13	13
173.0	0	17	17
174.0	0	12	12
175.0	0	14	14
176.0	0	16	16
177.0	0	16	16
178.0	0	11	11
179.0	0	19	19
180.0	0	18	18
181.0	0	15	15
182.0	0	9	9
183.0	0	7	7
184.0	0	7	7
185.0	0	17	17
186.0	0	8	8
187.0	0	10	10
188.0	0	9	9
189.0	0	7	7
190.0	0	12	12
191.0	0	16	16
192.0	0	9	9
193.0	0	8	8
194.0	0	11	11
195.0	0	11	11
196.0	0	11	11
197.0	0	9	9
198.0	0	7	7
199.0	0	7	7
200.0	0	14	14
201.0	0	15	15
202.0	0	11	11
203.0	0	7	7
204.0	0	8	8
205.0	0	5	5
206.0	0	12	12
207.0	0	11	11
208.0	0	7	7
209.0	0	3	3
210.0	0	5	5
211.0	0	8	8
212.0	0	6	6
213.0	0	9	9
214.0	0	6	6
215.0	0	6	6
216.0	0	8	8
217.0	0	7	7
218.0	0	10	10
219.0	0	8	8
220.0	0	7	7
221.0	0	10	10
222.0	0	5	5
223.0	0	8	8
224.0	0	9	9
225.0	0	8	8
226.0	0	11	11
227.0	0	6	6
228.0	0	11	11
229.0	0	5	5
230.0	0	12	12
231.0	0	9	9
232.0	0	7	7
233.0	0	6	6
234.0	0	8	8
235.0	0	7	7
236.0	0	6	6
237.0	0	5	5
238.0	0	6	6
239.0	0	6	6
240.0	0	11	11
241.0	0	10	10
242.0	0	6	6
243.0	0	5	5
244.0	0	4	4
245.0	0	5	5
246.0	0	5	5
247.0	0	6	6
248.0	0	3	3
249.0	0	2	2
250.0	0	7	7
251.0	0	3	3
252.0	0	4	4
253.0	0	6	6
254.0	0	7	7
255.0	0	11	11
256.0	0	5	5
257.0	0	3	3
258.0	0	10	10
259.0	0	6	6
260.0	0	2	2
261.0	0	4	4
262.0	0	3	3
263.0	0	13	13
264.0	0	4	4
265.0	0	5	5
266.0	0	9	9
267.0	0	5	5
268.0	0	8	8
269.0	0	2	2
270.0	0	8	8
271.0	0	6	6
272.0	0	5	5
273.0	0	7	7
274.0	0	3	3
275.0	0	5	5
276.0	0	3	3
277.0	0	7	7
278.0	0	6	6
279.0	0	3	3
280.0	0	3	3
281.0	0	3	3
282.0	0	2	2
283.0	0	8	8
284.0	0	3	3
285.0	0	4	4
286.0	0	3	3
287.0	0	6	6
288.0	0	4	4
289.0	0	1	1
290.0	0	1	1
291.0	0	6	6
292.0	0	4	4
293.0	0	3	3
294.0	0	8	8
295.0	0	2	2
296.0	0	4	4
297.0	0	4	4
298.0	0	3	3
299.0	0	4	4
300.0	0	2	2
301.0	0	6	6
302.0	0	2	2
303.0	0	6	6
304.0	0	2	2
305.0	0	4	4
306.0	0	6	6
307.0	0	3	3
308.0	0	1	1
309.0	0	2	2
310.0	0	3	3
311.0	0	2	2
312.0	0	4	4
313.0	0	2	2
314.0	0	5	5
315.0	0	4	4
316.0	0	3	3
317.0	0	2	2
318.0	0	3	3
319.0	0	2	2
320.0	0	5	5
321.0	0	2	2
322.0	0	2	2
323.0	0	4	4
324.0	0	3	3
325.0	0	4	4
326.0	0	5	5
327.0	0	1	1
328.0	0	4	4
329.0	0	3	3
330.0	0	4	4
331.0	0	1	1
332.0	0	4	4
333.0	0	2	2
335.0	0	6	6
336.0	0	4	4
337.0	0	2	2
338.0	0	2	2
339.0	0	3	3
340.0	0	4	4
341.0	0	1	1
342.0	0	4	4
343.0	0	2	2
344.0	0	1	1
345.0	0	1	1
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
349.0	0	2	2
350.0	0	2	2
351.0	0	4	4
352.0	0	1	1
354.0	0	3	3
356.0	0	2	2
357.0	0	1	1
358.0	0	3	3
359.0	0	4	4
360.0	0	3	3
361.0	0	2	2
362.0	0	6	6
363.0	0	3	3
364.0	0	1	1
365.0	0	2	2
366.0	0	1	1
367.0	0	2	2
368.0	0	5	5
369.0	0	1	1
370.0	0	2	2
371.0	0	5	5
372.0	0	3	3
373.0	0	1	1
374.0	0	1	1
376.0	0	1	1
377.0	0	4	4
378.0	0	1	1
379.0	0	4	4
380.0	0	3	3
381.0	0	1	1
382.0	0	3	3
383.0	0	4	4
385.0	0	1	1
386.0	0	2	2
387.0	0	1	1
388.0	0	2	2
389.0	0	1	1
390.0	0	1	1
391.0	0	6	6
393.0	0	1	1
394.0	0	1	1
396.0	0	1	1
397.0	0	3	3
398.0	0	2	2
399.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
405.0	0	2	2
406.0	0	1	1
407.0	0	3	3
408.0	0	1	1
409.0	0	2	2
410.0	0	1	1
411.0	0	2	2
413.0	0	2	2
415.0	0	3	3
416.0	0	3	3
417.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
423.0	0	2	2
424.0	0	2	2
425.0	0	3	3
426.0	0	3	3
427.0	0	3	3
428.0	0	3	3
431.0	0	1	1
433.0	0	2	2
434.0	0	2	2
435.0	0	1	1
436.0	0	4	4
437.0	0	2	2
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
445.0	0	2	2
448.0	0	3	3
450.0	0	1	1
451.0	0	1	1
452.0	0	2	2
453.0	0	2	2
455.0	0	2	2
456.0	0	3	3
457.0	0	1	1
459.0	0	2	2
463.0	0	2	2
464.0	0	1	1
468.0	0	3	3
469.0	0	1	1
470.0	0	1	1
471.0	0	1	1
472.0	0	1	1
473.0	0	1	1
476.0	0	2	2
477.0	0	2	2
479.0	0	3	3
483.0	0	2	2
484.0	0	5	5
485.0	0	2	2
486.0	0	2	2
489.0	0	1	1
490.0	0	1	1
491.0	0	1	1
492.0	0	3	3
493.0	0	1	1
495.0	0	1	1
498.0	0	1	1
500.0	0	2	2
501.0	0	1	1
503.0	0	1	1
505.0	0	2	2
506.0	0	2	2
507.0	0	2	2
508.0	0	1	1
509.0	0	2	2
512.0	0	1	1
516.0	0	2	2
518.0	0	1	1
520.0	0	5	5
529.0	0	3	3
530.0	0	1	1
533.0	0	1	1
535.0	0	1	1
536.0	0	1	1
537.0	0	1	1
539.0	0	2	2
540.0	0	1	1
541.0	0	1	1
542.0	0	3	3
543.0	0	1	1
545.0	0	2	2
547.0	0	1	1
548.0	0	3	3
553.0	0	1	1
554.0	0	1	1
557.0	0	1	1
558.0	0	2	2
560.0	0	1	1
562.0	0	2	2
563.0	0	1	1
565.0	0	1	1
570.0	0	1	1
572.0	0	3	3
577.0	0	1	1
583.0	0	1	1
585.0	0	2	2
586.0	0	1	1
590.0	0	1	1
591.0	0	2	2
592.0	0	1	1
595.0	0	1	1
597.0	0	1	1
598.0	0	1	1
601.0	0	1	1
603.0	0	1	1
607.0	0	1	1
609.0	0	1	1
610.0	0	1	1
611.0	0	1	1
614.0	0	1	1
616.0	0	1	1
617.0	0	1	1
622.0	0	2	2
624.0	0	1	1
626.0	0	1	1
634.0	0	1	1
635.0	0	1	1
637.0	0	1	1
638.0	0	1	1
640.0	0	2	2
643.0	0	1	1
645.0	0	1	1
648.0	0	1	1
649.0	0	3	3
654.0	0	1	1
657.0	0	1	1
660.0	0	1	1
665.0	0	1	1
667.0	0	2	2
669.0	0	1	1
672.0	0	1	1
676.0	0	1	1
685.0	0	1	1
686.0	0	2	2
687.0	0	2	2
689.0	0	1	1
693.0	0	1	1
695.0	0	1	1
698.0	0	1	1
700.0	0	2	2
705.0	0	1	1
706.0	0	1	1
710.0	0	2	2
712.0	0	2	2
713.0	0	1	1
718.0	0	2	2
729.0	0	1	1
734.0	0	1	1
735.0	0	1	1
736.0	0	1	1
740.0	0	1	1
745.0	0	1	1
755.0	0	1	1
761.0	0	1	1
770.0	0	1	1
771.0	0	1	1
772.0	0	1	1
773.0	0	1	1
777.0	0	1	1
786.0	0	2	2
801.0	0	1	1
803.0	0	2	2
809.0	0	1	1
811.0	0	1	1
815.0	0	1	1
816.0	0	1	1
817.0	0	1	1
826.0	0	1	1
827.0	0	1	1
830.0	0	2	2
850.0	0	1	1
851.0	0	1	1
857.0	0	1	1
870.0	0	1	1
872.0	0	1	1
876.0	0	1	1
885.0	0	1	1
887.0	0	2	2
902.0	0	1	1
913.0	0	1	1
917.0	0	1	1
923.0	0	1	1
927.0	0	1	1
933.0	0	2	2
941.0	0	1	1
942.0	0	1	1
957.0	0	1	1
984.0	0	1	1
994.0	0	1	1
1003.0	0	1	1
1010.0	0	1	1
1020.0	0	1	1
1022.0	0	1	1
1023.0	0	1	1
1026.0	0	1	1
1028.0	0	1	1
1038.0	0	1	1
1064.0	0	1	1
1068.0	0	1	1
1069.0	0	1	1
1070.0	0	1	1
1073.0	0	1	1
1079.0	0	1	1
1086.0	0	1	1
1087.0	0	1	1
1088.0	0	1	1
1089.0	0	1	1
1091.0	0	2	2
1120.0	0	1	1
1155.0	0	1	1
1173.0	0	1	1
1186.0	0	1	1
1191.0	0	1	1
1209.0	0	1	1
1224.0	0	1	1
1241.0	0	1	1
1268.0	0	1	1
1287.0	0	1	1
1291.0	0	1	1
1323.0	0	1	1
1332.0	0	1	1
1333.0	0	1	1
1346.0	0	1	1
1391.0	0	1	1
1420.0	0	1	1
1430.0	0	1	1
1443.0	0	1	1
1448.0	0	1	1
1449.0	0	1	1
1568.0	0	1	1
1583.0	0	1	1
1617.0	0	1	1
1638.0	0	1	1
1756.0	0	1	1
1769.0	0	1	1
1772.0	0	1	1
1785.0	0	1	1
1816.0	0	1	1
1848.0	0	1	1
1895.0	0	1	1
1986.0	0	1	1
2077.0	0	1	1
2210.0	0	1	1
2235.0	0	1	1
2269.0	0	1	1
2279.0	0	1	1
2469.0	0	1	1
2534.0	0	1	1
2598.0	0	1	1
3002.0	0	1	1
4079.0	0	1	1
5476.0	0	1	1