## 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-TA_1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-TA_1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-TA_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 22:52:35 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	1161713	45883546	0	1336301	886154	9509683	0	0.214202	94801654

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32198021	32198021
2.0	1.616316	3030584	3030584
3.0	1.996162	542386	542386
4.0	2.230267	201499	201499
5.0	2.374549	107573	107573
6.0	2.463473	66228	66228
7.0	2.518278	44504	44504
8.0	2.552056	31711	31711
9.0	2.572873	23382	23382
10.0	2.585703	18157	18157
11.0	2.593611	14384	14384
12.0	2.598484	11256	11256
13.0	2.601488	9365	9365
14.0	2.603339	7739	7739
15.0	2.60448	6396	6396
16.0	2.605183	5563	5563
17.0	2.605616	4765	4765
18.0	2.605883	4031	4031
19.0	2.606048	3523	3523
20.0	2.60615	3162	3162
21.0	2.606212	2703	2703
22.0	2.606251	2419	2419
23.0	2.606274	2147	2147
24.0	2.606289	1844	1844
25.0	2.606298	1814	1814
26.0	2.606304	1636	1636
27.0	2.606307	1485	1485
28.0	2.606309	1319	1319
29.0	2.60631	1243	1243
30.0	2.606311	1078	1078
31.0	2.606312	1025	1025
32.0	2.606312	966	966
33.0	2.606312	870	870
34.0	2.606312	797	797
35.0	2.606312	741	741
36.0	2.606312	668	668
37.0	2.606312	629	629
38.0	2.606312	632	632
39.0	2.606312	522	522
40.0	2.606312	539	539
41.0	2.606312	478	478
42.0	2.606313	497	497
43.0	2.606313	464	464
44.0	2.606313	377	377
45.0	2.606313	394	394
46.0	2.606313	392	392
47.0	2.606313	343	343
48.0	2.606313	365	365
49.0	2.606313	294	294
50.0	2.606313	322	322
51.0	2.606313	300	300
52.0	2.606313	296	296
53.0	2.606313	271	271
54.0	2.606313	228	228
55.0	2.606313	246	246
56.0	2.606313	234	234
57.0	2.606313	238	238
58.0	2.606313	229	229
59.0	2.606313	236	236
60.0	2.606313	206	206
61.0	2.606313	185	185
62.0	2.606313	179	179
63.0	2.606313	161	161
64.0	2.606313	159	159
65.0	2.606313	159	159
66.0	2.606313	162	162
67.0	2.606313	156	156
68.0	2.606313	130	130
69.0	2.606313	134	134
70.0	2.606313	138	138
71.0	2.606313	158	158
72.0	2.606313	125	125
73.0	2.606313	118	118
74.0	2.606313	109	109
75.0	2.606313	115	115
76.0	2.606313	115	115
77.0	2.606313	116	116
78.0	2.606313	114	114
79.0	2.606313	89	89
80.0	2.606313	103	103
81.0	2.606313	76	76
82.0	2.606313	87	87
83.0	2.606313	85	85
84.0	2.606313	99	99
85.0	2.606313	86	86
86.0	2.606313	81	81
87.0	2.606313	69	69
88.0	2.606313	72	72
89.0	2.606313	73	73
90.0	2.606313	71	71
91.0	2.606313	68	68
92.0	2.606313	76	76
93.0	2.606313	58	58
94.0	2.606313	66	66
95.0	2.606313	67	67
96.0	2.606313	53	53
97.0	2.606313	53	53
98.0	2.606313	72	72
99.0	2.606313	70	70
100.0	2.606313	64	64
101.0	0	61	61
102.0	0	66	66
103.0	0	42	42
104.0	0	66	66
105.0	0	39	39
106.0	0	45	45
107.0	0	47	47
108.0	0	50	50
109.0	0	48	48
110.0	0	32	32
111.0	0	49	49
112.0	0	51	51
113.0	0	42	42
114.0	0	45	45
115.0	0	39	39
116.0	0	35	35
117.0	0	48	48
118.0	0	50	50
119.0	0	40	40
120.0	0	40	40
121.0	0	30	30
122.0	0	34	34
123.0	0	34	34
124.0	0	40	40
125.0	0	34	34
126.0	0	25	25
127.0	0	43	43
128.0	0	30	30
129.0	0	32	32
130.0	0	21	21
131.0	0	34	34
132.0	0	31	31
133.0	0	21	21
134.0	0	22	22
135.0	0	28	28
136.0	0	40	40
137.0	0	30	30
138.0	0	23	23
139.0	0	31	31
140.0	0	22	22
141.0	0	22	22
142.0	0	25	25
143.0	0	20	20
144.0	0	30	30
145.0	0	26	26
146.0	0	31	31
147.0	0	29	29
148.0	0	24	24
149.0	0	15	15
150.0	0	20	20
151.0	0	22	22
152.0	0	17	17
153.0	0	15	15
154.0	0	17	17
155.0	0	11	11
156.0	0	26	26
157.0	0	22	22
158.0	0	22	22
159.0	0	16	16
160.0	0	11	11
161.0	0	14	14
162.0	0	18	18
163.0	0	10	10
164.0	0	16	16
165.0	0	21	21
166.0	0	13	13
167.0	0	17	17
168.0	0	25	25
169.0	0	16	16
170.0	0	13	13
171.0	0	15	15
172.0	0	11	11
173.0	0	16	16
174.0	0	16	16
175.0	0	17	17
176.0	0	13	13
177.0	0	7	7
178.0	0	19	19
179.0	0	11	11
180.0	0	16	16
181.0	0	13	13
182.0	0	16	16
183.0	0	23	23
184.0	0	20	20
185.0	0	14	14
186.0	0	10	10
187.0	0	11	11
188.0	0	12	12
189.0	0	8	8
190.0	0	16	16
191.0	0	11	11
192.0	0	15	15
193.0	0	14	14
194.0	0	11	11
195.0	0	14	14
196.0	0	17	17
197.0	0	11	11
198.0	0	6	6
199.0	0	12	12
200.0	0	11	11
201.0	0	19	19
202.0	0	9	9
203.0	0	8	8
204.0	0	11	11
205.0	0	8	8
206.0	0	12	12
207.0	0	8	8
208.0	0	10	10
209.0	0	13	13
210.0	0	16	16
211.0	0	10	10
212.0	0	14	14
213.0	0	17	17
214.0	0	12	12
215.0	0	6	6
216.0	0	13	13
217.0	0	10	10
218.0	0	10	10
219.0	0	6	6
220.0	0	14	14
221.0	0	5	5
222.0	0	10	10
223.0	0	8	8
224.0	0	9	9
225.0	0	11	11
226.0	0	5	5
227.0	0	7	7
228.0	0	6	6
229.0	0	8	8
230.0	0	9	9
231.0	0	7	7
232.0	0	6	6
233.0	0	5	5
234.0	0	8	8
235.0	0	11	11
236.0	0	11	11
237.0	0	6	6
238.0	0	5	5
239.0	0	11	11
240.0	0	10	10
241.0	0	6	6
242.0	0	8	8
243.0	0	7	7
244.0	0	6	6
245.0	0	8	8
246.0	0	5	5
247.0	0	6	6
248.0	0	9	9
249.0	0	4	4
250.0	0	5	5
251.0	0	10	10
252.0	0	7	7
253.0	0	4	4
254.0	0	6	6
255.0	0	6	6
256.0	0	6	6
257.0	0	5	5
258.0	0	6	6
259.0	0	3	3
260.0	0	3	3
261.0	0	3	3
262.0	0	8	8
263.0	0	3	3
264.0	0	5	5
265.0	0	4	4
266.0	0	8	8
267.0	0	2	2
268.0	0	2	2
269.0	0	3	3
270.0	0	5	5
271.0	0	4	4
272.0	0	4	4
273.0	0	8	8
274.0	0	3	3
275.0	0	7	7
276.0	0	5	5
277.0	0	6	6
278.0	0	6	6
279.0	0	2	2
280.0	0	2	2
281.0	0	3	3
282.0	0	2	2
283.0	0	1	1
284.0	0	2	2
285.0	0	4	4
286.0	0	5	5
287.0	0	1	1
288.0	0	3	3
289.0	0	5	5
290.0	0	3	3
291.0	0	5	5
292.0	0	5	5
293.0	0	2	2
294.0	0	7	7
295.0	0	3	3
296.0	0	5	5
297.0	0	7	7
298.0	0	4	4
299.0	0	2	2
300.0	0	1	1
301.0	0	8	8
302.0	0	2	2
303.0	0	6	6
304.0	0	4	4
305.0	0	3	3
306.0	0	5	5
307.0	0	2	2
308.0	0	4	4
309.0	0	3	3
310.0	0	1	1
311.0	0	3	3
312.0	0	4	4
313.0	0	1	1
314.0	0	2	2
315.0	0	4	4
316.0	0	2	2
317.0	0	5	5
318.0	0	8	8
319.0	0	2	2
320.0	0	1	1
321.0	0	3	3
322.0	0	4	4
323.0	0	5	5
324.0	0	2	2
325.0	0	1	1
326.0	0	4	4
327.0	0	2	2
328.0	0	2	2
329.0	0	6	6
330.0	0	5	5
331.0	0	4	4
332.0	0	2	2
333.0	0	6	6
334.0	0	9	9
335.0	0	2	2
336.0	0	1	1
337.0	0	6	6
338.0	0	2	2
339.0	0	3	3
340.0	0	2	2
341.0	0	4	4
342.0	0	1	1
343.0	0	2	2
344.0	0	7	7
345.0	0	5	5
346.0	0	2	2
347.0	0	5	5
348.0	0	2	2
349.0	0	3	3
350.0	0	1	1
351.0	0	3	3
352.0	0	4	4
353.0	0	4	4
354.0	0	3	3
355.0	0	3	3
356.0	0	2	2
357.0	0	2	2
358.0	0	4	4
359.0	0	4	4
360.0	0	4	4
361.0	0	5	5
362.0	0	2	2
363.0	0	2	2
364.0	0	3	3
365.0	0	3	3
366.0	0	2	2
368.0	0	2	2
369.0	0	4	4
370.0	0	2	2
371.0	0	4	4
372.0	0	1	1
373.0	0	1	1
374.0	0	4	4
375.0	0	4	4
376.0	0	7	7
377.0	0	2	2
378.0	0	2	2
379.0	0	3	3
380.0	0	2	2
381.0	0	3	3
382.0	0	1	1
383.0	0	3	3
384.0	0	1	1
385.0	0	1	1
386.0	0	3	3
387.0	0	2	2
388.0	0	1	1
389.0	0	3	3
390.0	0	1	1
391.0	0	3	3
392.0	0	2	2
393.0	0	4	4
394.0	0	1	1
396.0	0	3	3
397.0	0	2	2
398.0	0	3	3
399.0	0	4	4
400.0	0	2	2
401.0	0	1	1
402.0	0	3	3
403.0	0	3	3
404.0	0	2	2
405.0	0	5	5
406.0	0	4	4
407.0	0	3	3
408.0	0	1	1
409.0	0	3	3
410.0	0	3	3
411.0	0	1	1
413.0	0	1	1
414.0	0	3	3
415.0	0	1	1
419.0	0	2	2
420.0	0	2	2
421.0	0	2	2
422.0	0	3	3
423.0	0	2	2
424.0	0	2	2
425.0	0	1	1
426.0	0	3	3
427.0	0	2	2
429.0	0	1	1
430.0	0	4	4
431.0	0	1	1
434.0	0	1	1
435.0	0	3	3
436.0	0	5	5
437.0	0	1	1
438.0	0	1	1
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
442.0	0	4	4
443.0	0	2	2
444.0	0	2	2
445.0	0	2	2
446.0	0	1	1
447.0	0	1	1
448.0	0	1	1
449.0	0	1	1
451.0	0	2	2
452.0	0	1	1
454.0	0	3	3
455.0	0	1	1
457.0	0	1	1
458.0	0	3	3
459.0	0	3	3
461.0	0	1	1
462.0	0	2	2
463.0	0	1	1
464.0	0	2	2
465.0	0	1	1
467.0	0	1	1
468.0	0	1	1
469.0	0	1	1
470.0	0	2	2
473.0	0	2	2
474.0	0	3	3
475.0	0	2	2
477.0	0	3	3
478.0	0	2	2
479.0	0	3	3
481.0	0	1	1
482.0	0	2	2
483.0	0	3	3
485.0	0	2	2
487.0	0	2	2
488.0	0	1	1
490.0	0	2	2
491.0	0	3	3
492.0	0	2	2
493.0	0	2	2
494.0	0	1	1
496.0	0	1	1
497.0	0	2	2
500.0	0	1	1
501.0	0	1	1
503.0	0	2	2
504.0	0	2	2
505.0	0	3	3
507.0	0	1	1
508.0	0	1	1
509.0	0	2	2
510.0	0	1	1
513.0	0	2	2
515.0	0	2	2
516.0	0	2	2
519.0	0	1	1
520.0	0	3	3
521.0	0	1	1
522.0	0	2	2
523.0	0	1	1
525.0	0	1	1
527.0	0	2	2
528.0	0	1	1
531.0	0	2	2
532.0	0	2	2
533.0	0	2	2
534.0	0	1	1
535.0	0	1	1
537.0	0	1	1
540.0	0	1	1
541.0	0	3	3
545.0	0	2	2
546.0	0	1	1
547.0	0	1	1
548.0	0	1	1
549.0	0	1	1
551.0	0	1	1
553.0	0	3	3
554.0	0	1	1
556.0	0	1	1
559.0	0	1	1
560.0	0	1	1
561.0	0	1	1
563.0	0	1	1
565.0	0	1	1
566.0	0	1	1
573.0	0	1	1
574.0	0	1	1
577.0	0	1	1
579.0	0	1	1
581.0	0	4	4
582.0	0	1	1
584.0	0	1	1
587.0	0	1	1
591.0	0	1	1
592.0	0	4	4
595.0	0	1	1
596.0	0	2	2
597.0	0	1	1
600.0	0	1	1
604.0	0	1	1
605.0	0	1	1
606.0	0	2	2
609.0	0	1	1
610.0	0	1	1
611.0	0	1	1
612.0	0	1	1
615.0	0	2	2
617.0	0	2	2
618.0	0	2	2
619.0	0	1	1
621.0	0	1	1
622.0	0	2	2
623.0	0	3	3
626.0	0	1	1
629.0	0	2	2
630.0	0	1	1
632.0	0	1	1
633.0	0	1	1
634.0	0	1	1
635.0	0	1	1
636.0	0	2	2
637.0	0	1	1
640.0	0	2	2
641.0	0	1	1
642.0	0	2	2
644.0	0	1	1
645.0	0	1	1
647.0	0	1	1
648.0	0	3	3
650.0	0	2	2
652.0	0	1	1
653.0	0	1	1
655.0	0	2	2
656.0	0	2	2
659.0	0	4	4
664.0	0	2	2
665.0	0	3	3
666.0	0	2	2
671.0	0	2	2
672.0	0	1	1
674.0	0	1	1
676.0	0	1	1
677.0	0	1	1
682.0	0	2	2
683.0	0	1	1
686.0	0	1	1
687.0	0	1	1
691.0	0	1	1
696.0	0	3	3
699.0	0	1	1
702.0	0	1	1
703.0	0	1	1
704.0	0	1	1
705.0	0	1	1
707.0	0	2	2
716.0	0	1	1
717.0	0	1	1
720.0	0	1	1
722.0	0	1	1
723.0	0	2	2
726.0	0	1	1
727.0	0	1	1
730.0	0	1	1
733.0	0	2	2
735.0	0	2	2
737.0	0	3	3
739.0	0	1	1
745.0	0	1	1
747.0	0	1	1
750.0	0	1	1
751.0	0	1	1
752.0	0	1	1
754.0	0	1	1
765.0	0	1	1
769.0	0	1	1
771.0	0	1	1
779.0	0	2	2
791.0	0	1	1
792.0	0	1	1
794.0	0	2	2
799.0	0	1	1
800.0	0	1	1
804.0	0	1	1
806.0	0	1	1
812.0	0	1	1
813.0	0	1	1
817.0	0	2	2
822.0	0	1	1
823.0	0	1	1
824.0	0	1	1
827.0	0	2	2
834.0	0	1	1
835.0	0	1	1
838.0	0	1	1
847.0	0	1	1
856.0	0	1	1
861.0	0	1	1
871.0	0	1	1
876.0	0	1	1
878.0	0	1	1
891.0	0	1	1
900.0	0	1	1
904.0	0	2	2
905.0	0	1	1
906.0	0	1	1
911.0	0	1	1
912.0	0	1	1
915.0	0	1	1
920.0	0	1	1
921.0	0	1	1
926.0	0	1	1
942.0	0	1	1
946.0	0	1	1
950.0	0	2	2
951.0	0	1	1
955.0	0	1	1
983.0	0	1	1
984.0	0	1	1
993.0	0	1	1
999.0	0	1	1
1001.0	0	1	1
1005.0	0	1	1
1007.0	0	1	1
1010.0	0	1	1
1017.0	0	2	2
1030.0	0	1	1
1034.0	0	1	1
1037.0	0	1	1
1040.0	0	1	1
1052.0	0	1	1
1074.0	0	1	1
1075.0	0	1	1
1092.0	0	1	1
1101.0	0	1	1
1113.0	0	1	1
1115.0	0	1	1
1121.0	0	1	1
1122.0	0	1	1
1129.0	0	1	1
1140.0	0	1	1
1142.0	0	1	1
1144.0	0	1	1
1149.0	0	1	1
1150.0	0	1	1
1153.0	0	1	1
1166.0	0	1	1
1200.0	0	1	1
1208.0	0	1	1
1211.0	0	1	1
1222.0	0	1	1
1224.0	0	1	1
1232.0	0	1	1
1246.0	0	1	1
1260.0	0	1	1
1312.0	0	1	1
1334.0	0	1	1
1349.0	0	1	1
1361.0	0	1	1
1363.0	0	1	1
1376.0	0	1	1
1443.0	0	2	2
1471.0	0	1	1
1488.0	0	1	1
1499.0	0	1	1
1503.0	0	1	1
1547.0	0	1	1
1548.0	0	1	1
1563.0	0	1	1
1564.0	0	1	1
1571.0	0	1	1
1578.0	0	1	1
1619.0	0	1	1
1632.0	0	1	1
1637.0	0	1	1
1713.0	0	1	1
1744.0	0	1	1
1795.0	0	1	1
1811.0	0	1	1
1838.0	0	1	1
1911.0	0	1	1
2031.0	0	1	1
2243.0	0	1	1
2287.0	0	1	1
2383.0	0	1	1
2413.0	0	1	1
2452.0	0	1	1
2552.0	0	1	1
2686.0	0	1	1
2699.0	0	2	2
2705.0	0	1	1
2769.0	0	1	1
2846.0	0	1	1
3081.0	0	1	1
3090.0	0	1	1
3091.0	0	1	1
3127.0	0	1	1
3223.0	0	1	1
3365.0	0	1	1
4998.0	0	1	1