## 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_plus_TA_100nM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_100nM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_TA_100nM_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 20:39:29 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	1000956	40543934	0	1153482	721847	6440582	0	0.165711	113707102

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31389223	31389223
2.0	1.700077	1922388	1922388
3.0	2.190185	358030	358030
4.0	2.533299	145343	145343
5.0	2.773505	78303	78303
6.0	2.941667	48202	48202
7.0	3.059394	32452	32452
8.0	3.141812	23178	23178
9.0	3.199511	16586	16586
10.0	3.239905	12830	12830
11.0	3.268183	9922	9922
12.0	3.287981	8105	8105
13.0	3.30184	6515	6515
14.0	3.311543	5199	5199
15.0	3.318336	4424	4424
16.0	3.323091	3654	3654
17.0	3.32642	3284	3284
18.0	3.328751	2811	2811
19.0	3.330383	2414	2414
20.0	3.331525	2152	2152
21.0	3.332325	1949	1949
22.0	3.332885	1717	1717
23.0	3.333277	1506	1506
24.0	3.333551	1380	1380
25.0	3.333743	1287	1287
26.0	3.333877	1099	1099
27.0	3.333972	1042	1042
28.0	3.334038	910	910
29.0	3.334084	843	843
30.0	3.334116	758	758
31.0	3.334139	750	750
32.0	3.334154	659	659
33.0	3.334166	574	574
34.0	3.334173	583	583
35.0	3.334179	510	510
36.0	3.334182	496	496
37.0	3.334185	453	453
38.0	3.334187	445	445
39.0	3.334188	400	400
40.0	3.334189	358	358
41.0	3.33419	344	344
42.0	3.33419	348	348
43.0	3.334191	288	288
44.0	3.334191	317	317
45.0	3.334191	295	295
46.0	3.334191	285	285
47.0	3.334191	268	268
48.0	3.334191	237	237
49.0	3.334191	229	229
50.0	3.334191	244	244
51.0	3.334191	221	221
52.0	3.334191	198	198
53.0	3.334191	192	192
54.0	3.334191	183	183
55.0	3.334191	188	188
56.0	3.334191	145	145
57.0	3.334191	153	153
58.0	3.334191	167	167
59.0	3.334191	146	146
60.0	3.334191	132	132
61.0	3.334191	141	141
62.0	3.334191	150	150
63.0	3.334191	148	148
64.0	3.334191	118	118
65.0	3.334191	115	115
66.0	3.334191	109	109
67.0	3.334191	114	114
68.0	3.334191	118	118
69.0	3.334191	90	90
70.0	3.334191	120	120
71.0	3.334191	91	91
72.0	3.334191	105	105
73.0	3.334191	106	106
74.0	3.334191	73	73
75.0	3.334191	85	85
76.0	3.334191	78	78
77.0	3.334191	84	84
78.0	3.334191	51	51
79.0	3.334191	72	72
80.0	3.334191	76	76
81.0	3.334191	65	65
82.0	3.334191	70	70
83.0	3.334191	69	69
84.0	3.334191	75	75
85.0	3.334191	70	70
86.0	3.334191	57	57
87.0	3.334191	56	56
88.0	3.334191	55	55
89.0	3.334191	75	75
90.0	3.334191	54	54
91.0	3.334191	47	47
92.0	3.334191	54	54
93.0	3.334191	53	53
94.0	3.334191	36	36
95.0	3.334191	43	43
96.0	3.334191	49	49
97.0	3.334191	56	56
98.0	3.334191	42	42
99.0	3.334191	55	55
100.0	3.334191	48	48
101.0	0	32	32
102.0	0	52	52
103.0	0	45	45
104.0	0	38	38
105.0	0	40	40
106.0	0	41	41
107.0	0	33	33
108.0	0	27	27
109.0	0	32	32
110.0	0	30	30
111.0	0	21	21
112.0	0	35	35
113.0	0	34	34
114.0	0	28	28
115.0	0	28	28
116.0	0	23	23
117.0	0	21	21
118.0	0	24	24
119.0	0	21	21
120.0	0	27	27
121.0	0	20	20
122.0	0	38	38
123.0	0	18	18
124.0	0	31	31
125.0	0	26	26
126.0	0	32	32
127.0	0	30	30
128.0	0	25	25
129.0	0	22	22
130.0	0	16	16
131.0	0	28	28
132.0	0	19	19
133.0	0	27	27
134.0	0	28	28
135.0	0	26	26
136.0	0	20	20
137.0	0	18	18
138.0	0	23	23
139.0	0	21	21
140.0	0	16	16
141.0	0	18	18
142.0	0	13	13
143.0	0	19	19
144.0	0	17	17
145.0	0	23	23
146.0	0	23	23
147.0	0	20	20
148.0	0	8	8
149.0	0	16	16
150.0	0	9	9
151.0	0	21	21
152.0	0	24	24
153.0	0	13	13
154.0	0	12	12
155.0	0	19	19
156.0	0	18	18
157.0	0	12	12
158.0	0	18	18
159.0	0	8	8
160.0	0	23	23
161.0	0	12	12
162.0	0	13	13
163.0	0	11	11
164.0	0	13	13
165.0	0	9	9
166.0	0	12	12
167.0	0	12	12
168.0	0	9	9
169.0	0	12	12
170.0	0	10	10
171.0	0	15	15
172.0	0	10	10
173.0	0	16	16
174.0	0	10	10
175.0	0	7	7
176.0	0	10	10
177.0	0	11	11
178.0	0	6	6
179.0	0	10	10
180.0	0	11	11
181.0	0	16	16
182.0	0	12	12
183.0	0	7	7
184.0	0	11	11
185.0	0	9	9
186.0	0	13	13
187.0	0	7	7
188.0	0	13	13
189.0	0	13	13
190.0	0	7	7
191.0	0	10	10
192.0	0	14	14
193.0	0	6	6
194.0	0	9	9
195.0	0	9	9
196.0	0	9	9
197.0	0	12	12
198.0	0	19	19
199.0	0	9	9
200.0	0	10	10
201.0	0	6	6
202.0	0	10	10
203.0	0	8	8
204.0	0	7	7
205.0	0	7	7
206.0	0	6	6
207.0	0	10	10
208.0	0	7	7
209.0	0	2	2
210.0	0	9	9
211.0	0	9	9
212.0	0	7	7
213.0	0	6	6
214.0	0	9	9
215.0	0	7	7
216.0	0	11	11
217.0	0	5	5
218.0	0	7	7
219.0	0	8	8
220.0	0	9	9
221.0	0	10	10
222.0	0	8	8
223.0	0	7	7
224.0	0	6	6
225.0	0	6	6
226.0	0	3	3
227.0	0	4	4
228.0	0	6	6
229.0	0	7	7
230.0	0	3	3
231.0	0	12	12
232.0	0	1	1
233.0	0	3	3
234.0	0	3	3
235.0	0	5	5
236.0	0	8	8
237.0	0	6	6
238.0	0	4	4
239.0	0	6	6
240.0	0	8	8
241.0	0	6	6
242.0	0	7	7
243.0	0	7	7
244.0	0	6	6
245.0	0	5	5
246.0	0	4	4
247.0	0	6	6
248.0	0	4	4
249.0	0	6	6
250.0	0	6	6
251.0	0	6	6
252.0	0	4	4
253.0	0	3	3
254.0	0	1	1
255.0	0	2	2
256.0	0	5	5
257.0	0	9	9
258.0	0	4	4
259.0	0	5	5
260.0	0	2	2
261.0	0	6	6
262.0	0	4	4
263.0	0	4	4
264.0	0	2	2
265.0	0	2	2
266.0	0	3	3
267.0	0	3	3
268.0	0	7	7
269.0	0	2	2
270.0	0	3	3
271.0	0	3	3
272.0	0	4	4
273.0	0	3	3
274.0	0	4	4
275.0	0	3	3
276.0	0	3	3
277.0	0	2	2
278.0	0	4	4
279.0	0	1	1
280.0	0	7	7
281.0	0	6	6
282.0	0	1	1
283.0	0	4	4
284.0	0	3	3
285.0	0	6	6
286.0	0	3	3
287.0	0	7	7
288.0	0	2	2
289.0	0	1	1
290.0	0	2	2
291.0	0	2	2
292.0	0	2	2
293.0	0	3	3
294.0	0	1	1
295.0	0	4	4
296.0	0	4	4
297.0	0	3	3
298.0	0	2	2
299.0	0	4	4
300.0	0	1	1
301.0	0	1	1
302.0	0	5	5
304.0	0	1	1
305.0	0	2	2
306.0	0	3	3
307.0	0	3	3
308.0	0	4	4
309.0	0	1	1
310.0	0	4	4
311.0	0	1	1
312.0	0	3	3
313.0	0	2	2
314.0	0	3	3
316.0	0	3	3
317.0	0	4	4
319.0	0	3	3
320.0	0	3	3
321.0	0	5	5
322.0	0	3	3
323.0	0	2	2
324.0	0	1	1
325.0	0	5	5
326.0	0	1	1
328.0	0	1	1
329.0	0	2	2
330.0	0	3	3
331.0	0	2	2
332.0	0	2	2
333.0	0	4	4
334.0	0	3	3
335.0	0	1	1
336.0	0	1	1
337.0	0	5	5
338.0	0	2	2
339.0	0	2	2
340.0	0	1	1
341.0	0	2	2
342.0	0	1	1
343.0	0	2	2
344.0	0	1	1
345.0	0	1	1
346.0	0	4	4
347.0	0	2	2
348.0	0	2	2
349.0	0	3	3
350.0	0	1	1
351.0	0	1	1
352.0	0	2	2
353.0	0	3	3
355.0	0	2	2
356.0	0	3	3
357.0	0	1	1
358.0	0	2	2
360.0	0	1	1
361.0	0	1	1
362.0	0	2	2
363.0	0	1	1
364.0	0	6	6
365.0	0	1	1
366.0	0	2	2
367.0	0	1	1
368.0	0	3	3
369.0	0	5	5
370.0	0	2	2
371.0	0	3	3
372.0	0	1	1
373.0	0	3	3
374.0	0	3	3
375.0	0	3	3
376.0	0	1	1
377.0	0	2	2
378.0	0	3	3
379.0	0	1	1
380.0	0	2	2
381.0	0	1	1
382.0	0	4	4
383.0	0	1	1
384.0	0	1	1
387.0	0	4	4
388.0	0	5	5
390.0	0	3	3
391.0	0	1	1
393.0	0	2	2
394.0	0	3	3
395.0	0	3	3
396.0	0	4	4
399.0	0	3	3
400.0	0	3	3
402.0	0	2	2
404.0	0	2	2
405.0	0	1	1
406.0	0	2	2
407.0	0	1	1
410.0	0	4	4
411.0	0	1	1
412.0	0	2	2
414.0	0	3	3
415.0	0	1	1
418.0	0	2	2
419.0	0	1	1
420.0	0	1	1
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
426.0	0	1	1
429.0	0	1	1
431.0	0	3	3
432.0	0	2	2
434.0	0	2	2
435.0	0	1	1
436.0	0	1	1
437.0	0	3	3
440.0	0	1	1
442.0	0	2	2
444.0	0	1	1
446.0	0	1	1
448.0	0	2	2
449.0	0	2	2
450.0	0	2	2
451.0	0	3	3
452.0	0	1	1
455.0	0	2	2
458.0	0	1	1
459.0	0	1	1
462.0	0	1	1
464.0	0	1	1
465.0	0	1	1
468.0	0	3	3
470.0	0	1	1
472.0	0	1	1
474.0	0	2	2
479.0	0	1	1
482.0	0	1	1
483.0	0	2	2
484.0	0	1	1
488.0	0	3	3
489.0	0	1	1
492.0	0	2	2
494.0	0	1	1
496.0	0	1	1
498.0	0	1	1
503.0	0	1	1
504.0	0	1	1
507.0	0	1	1
508.0	0	1	1
510.0	0	1	1
513.0	0	2	2
514.0	0	1	1
516.0	0	1	1
520.0	0	2	2
521.0	0	1	1
523.0	0	1	1
524.0	0	1	1
528.0	0	1	1
529.0	0	1	1
530.0	0	3	3
531.0	0	1	1
532.0	0	1	1
534.0	0	2	2
542.0	0	1	1
544.0	0	2	2
545.0	0	1	1
547.0	0	2	2
549.0	0	1	1
551.0	0	1	1
552.0	0	1	1
557.0	0	1	1
559.0	0	1	1
560.0	0	1	1
565.0	0	1	1
571.0	0	2	2
574.0	0	1	1
575.0	0	1	1
579.0	0	1	1
583.0	0	3	3
585.0	0	1	1
586.0	0	1	1
592.0	0	1	1
596.0	0	2	2
597.0	0	2	2
598.0	0	1	1
600.0	0	1	1
606.0	0	1	1
607.0	0	1	1
611.0	0	1	1
613.0	0	1	1
615.0	0	1	1
617.0	0	1	1
621.0	0	2	2
623.0	0	2	2
625.0	0	1	1
632.0	0	1	1
633.0	0	1	1
635.0	0	1	1
636.0	0	3	3
638.0	0	1	1
639.0	0	2	2
642.0	0	1	1
643.0	0	1	1
645.0	0	1	1
648.0	0	1	1
649.0	0	1	1
650.0	0	2	2
651.0	0	1	1
652.0	0	1	1
653.0	0	1	1
655.0	0	4	4
656.0	0	1	1
664.0	0	1	1
672.0	0	1	1
678.0	0	1	1
679.0	0	1	1
681.0	0	1	1
686.0	0	1	1
691.0	0	1	1
692.0	0	1	1
694.0	0	1	1
704.0	0	1	1
711.0	0	1	1
714.0	0	1	1
718.0	0	1	1
723.0	0	2	2
724.0	0	1	1
725.0	0	1	1
731.0	0	1	1
732.0	0	1	1
734.0	0	1	1
746.0	0	2	2
748.0	0	1	1
752.0	0	1	1
760.0	0	1	1
764.0	0	1	1
766.0	0	1	1
775.0	0	1	1
778.0	0	1	1
779.0	0	1	1
786.0	0	1	1
799.0	0	1	1
820.0	0	1	1
832.0	0	1	1
833.0	0	3	3
834.0	0	1	1
847.0	0	1	1
850.0	0	1	1
853.0	0	1	1
862.0	0	1	1
877.0	0	1	1
880.0	0	1	1
881.0	0	1	1
888.0	0	1	1
893.0	0	1	1
895.0	0	1	1
900.0	0	1	1
902.0	0	1	1
923.0	0	1	1
925.0	0	1	1
928.0	0	1	1
931.0	0	1	1
936.0	0	1	1
946.0	0	1	1
952.0	0	1	1
962.0	0	1	1
967.0	0	1	1
983.0	0	1	1
997.0	0	1	1
1017.0	0	1	1
1021.0	0	1	1
1025.0	0	1	1
1027.0	0	1	1
1038.0	0	1	1
1040.0	0	1	1
1046.0	0	1	1
1048.0	0	1	1
1053.0	0	1	1
1063.0	0	1	1
1067.0	0	1	1
1074.0	0	1	1
1080.0	0	1	1
1085.0	0	1	1
1087.0	0	1	1
1097.0	0	1	1
1122.0	0	1	1
1127.0	0	1	1
1135.0	0	1	1
1140.0	0	1	1
1157.0	0	1	1
1159.0	0	1	1
1160.0	0	1	1
1171.0	0	1	1
1217.0	0	1	1
1233.0	0	1	1
1248.0	0	1	1
1268.0	0	1	1
1276.0	0	1	1
1288.0	0	1	1
1293.0	0	1	1
1306.0	0	1	1
1351.0	0	1	1
1361.0	0	1	1
1533.0	0	1	1
1574.0	0	1	1
1618.0	0	1	1
1650.0	0	1	1
1697.0	0	1	1
1810.0	0	1	1
2200.0	0	1	1