## 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_100nM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-TA_100nM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-TA_100nM_1.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 21:04:05 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	1504759	66905992	0	1725093	1219337	14495367	0	0.223254	131191986

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	47255785	47255785
2.0	1.600504	3342746	3342746
3.0	1.96111	755462	755462
4.0	2.177655	330686	330686
5.0	2.307691	186144	186144
6.0	2.385779	116973	116973
7.0	2.432671	79765	79765
8.0	2.460829	57497	57497
9.0	2.477739	43017	43017
10.0	2.487893	33148	33148
11.0	2.493991	26527	26527
12.0	2.497652	21565	21565
13.0	2.499851	17714	17714
14.0	2.501172	14550	14550
15.0	2.501964	12302	12302
16.0	2.502441	10422	10422
17.0	2.502727	8899	8899
18.0	2.502898	7892	7892
19.0	2.503001	6950	6950
20.0	2.503063	6053	6053
21.0	2.5031	5362	5362
22.0	2.503123	4686	4686
23.0	2.503136	4230	4230
24.0	2.503144	3826	3826
25.0	2.503149	3480	3480
26.0	2.503152	3121	3121
27.0	2.503154	2846	2846
28.0	2.503155	2561	2561
29.0	2.503155	2332	2332
30.0	2.503156	2210	2210
31.0	2.503156	2084	2084
32.0	2.503156	1856	1856
33.0	2.503156	1742	1742
34.0	2.503156	1622	1622
35.0	2.503156	1480	1480
36.0	2.503156	1361	1361
37.0	2.503156	1291	1291
38.0	2.503156	1220	1220
39.0	2.503156	1104	1104
40.0	2.503156	1081	1081
41.0	2.503156	1012	1012
42.0	2.503156	893	893
43.0	2.503156	851	851
44.0	2.503156	888	888
45.0	2.503156	770	770
46.0	2.503156	748	748
47.0	2.503156	701	701
48.0	2.503156	648	648
49.0	2.503156	598	598
50.0	2.503156	617	617
51.0	2.503156	543	543
52.0	2.503156	567	567
53.0	2.503156	497	497
54.0	2.503156	545	545
55.0	2.503156	450	450
56.0	2.503156	483	483
57.0	2.503156	430	430
58.0	2.503156	404	404
59.0	2.503156	387	387
60.0	2.503156	401	401
61.0	2.503156	374	374
62.0	2.503156	327	327
63.0	2.503156	312	312
64.0	2.503156	309	309
65.0	2.503156	293	293
66.0	2.503156	277	277
67.0	2.503156	291	291
68.0	2.503156	249	249
69.0	2.503156	265	265
70.0	2.503156	254	254
71.0	2.503156	240	240
72.0	2.503156	221	221
73.0	2.503156	221	221
74.0	2.503156	214	214
75.0	2.503156	219	219
76.0	2.503156	202	202
77.0	2.503156	219	219
78.0	2.503156	182	182
79.0	2.503156	182	182
80.0	2.503156	187	187
81.0	2.503156	180	180
82.0	2.503156	162	162
83.0	2.503156	175	175
84.0	2.503156	153	153
85.0	2.503156	154	154
86.0	2.503156	153	153
87.0	2.503156	156	156
88.0	2.503156	138	138
89.0	2.503156	142	142
90.0	2.503156	149	149
91.0	2.503156	127	127
92.0	2.503156	117	117
93.0	2.503156	141	141
94.0	2.503156	120	120
95.0	2.503156	132	132
96.0	2.503156	120	120
97.0	2.503156	102	102
98.0	2.503156	104	104
99.0	2.503156	113	113
100.0	2.503156	120	120
101.0	0	105	105
102.0	0	97	97
103.0	0	97	97
104.0	0	101	101
105.0	0	89	89
106.0	0	90	90
107.0	0	109	109
108.0	0	94	94
109.0	0	85	85
110.0	0	88	88
111.0	0	85	85
112.0	0	71	71
113.0	0	64	64
114.0	0	76	76
115.0	0	74	74
116.0	0	75	75
117.0	0	66	66
118.0	0	61	61
119.0	0	71	71
120.0	0	60	60
121.0	0	72	72
122.0	0	66	66
123.0	0	50	50
124.0	0	56	56
125.0	0	61	61
126.0	0	48	48
127.0	0	66	66
128.0	0	58	58
129.0	0	67	67
130.0	0	60	60
131.0	0	55	55
132.0	0	52	52
133.0	0	50	50
134.0	0	47	47
135.0	0	51	51
136.0	0	33	33
137.0	0	38	38
138.0	0	45	45
139.0	0	43	43
140.0	0	38	38
141.0	0	51	51
142.0	0	43	43
143.0	0	40	40
144.0	0	40	40
145.0	0	38	38
146.0	0	29	29
147.0	0	24	24
148.0	0	42	42
149.0	0	39	39
150.0	0	31	31
151.0	0	29	29
152.0	0	42	42
153.0	0	29	29
154.0	0	43	43
155.0	0	36	36
156.0	0	25	25
157.0	0	41	41
158.0	0	27	27
159.0	0	36	36
160.0	0	42	42
161.0	0	35	35
162.0	0	28	28
163.0	0	35	35
164.0	0	30	30
165.0	0	33	33
166.0	0	24	24
167.0	0	30	30
168.0	0	34	34
169.0	0	24	24
170.0	0	30	30
171.0	0	29	29
172.0	0	22	22
173.0	0	21	21
174.0	0	23	23
175.0	0	42	42
176.0	0	29	29
177.0	0	21	21
178.0	0	38	38
179.0	0	27	27
180.0	0	26	26
181.0	0	16	16
182.0	0	22	22
183.0	0	24	24
184.0	0	27	27
185.0	0	14	14
186.0	0	29	29
187.0	0	20	20
188.0	0	29	29
189.0	0	23	23
190.0	0	18	18
191.0	0	22	22
192.0	0	19	19
193.0	0	17	17
194.0	0	26	26
195.0	0	23	23
196.0	0	22	22
197.0	0	31	31
198.0	0	19	19
199.0	0	17	17
200.0	0	23	23
201.0	0	22	22
202.0	0	28	28
203.0	0	14	14
204.0	0	21	21
205.0	0	18	18
206.0	0	27	27
207.0	0	20	20
208.0	0	17	17
209.0	0	17	17
210.0	0	21	21
211.0	0	14	14
212.0	0	15	15
213.0	0	15	15
214.0	0	19	19
215.0	0	12	12
216.0	0	19	19
217.0	0	10	10
218.0	0	21	21
219.0	0	17	17
220.0	0	21	21
221.0	0	15	15
222.0	0	11	11
223.0	0	20	20
224.0	0	14	14
225.0	0	20	20
226.0	0	21	21
227.0	0	17	17
228.0	0	11	11
229.0	0	15	15
230.0	0	16	16
231.0	0	20	20
232.0	0	11	11
233.0	0	10	10
234.0	0	16	16
235.0	0	9	9
236.0	0	13	13
237.0	0	12	12
238.0	0	23	23
239.0	0	15	15
240.0	0	11	11
241.0	0	22	22
242.0	0	12	12
243.0	0	8	8
244.0	0	8	8
245.0	0	12	12
246.0	0	10	10
247.0	0	10	10
248.0	0	10	10
249.0	0	8	8
250.0	0	8	8
251.0	0	17	17
252.0	0	8	8
253.0	0	12	12
254.0	0	9	9
255.0	0	6	6
256.0	0	14	14
257.0	0	7	7
258.0	0	10	10
259.0	0	9	9
260.0	0	13	13
261.0	0	10	10
262.0	0	15	15
263.0	0	12	12
264.0	0	12	12
265.0	0	11	11
266.0	0	10	10
267.0	0	5	5
268.0	0	16	16
269.0	0	4	4
270.0	0	12	12
271.0	0	6	6
272.0	0	6	6
273.0	0	8	8
274.0	0	8	8
275.0	0	4	4
276.0	0	6	6
277.0	0	8	8
278.0	0	8	8
279.0	0	5	5
280.0	0	7	7
281.0	0	9	9
282.0	0	6	6
283.0	0	14	14
284.0	0	1	1
285.0	0	7	7
286.0	0	4	4
287.0	0	6	6
288.0	0	5	5
289.0	0	6	6
290.0	0	11	11
291.0	0	3	3
292.0	0	7	7
293.0	0	10	10
294.0	0	8	8
295.0	0	9	9
296.0	0	7	7
297.0	0	8	8
298.0	0	2	2
299.0	0	4	4
300.0	0	3	3
301.0	0	12	12
302.0	0	6	6
303.0	0	4	4
304.0	0	7	7
305.0	0	7	7
306.0	0	6	6
307.0	0	4	4
308.0	0	3	3
309.0	0	6	6
310.0	0	3	3
311.0	0	5	5
312.0	0	7	7
313.0	0	7	7
314.0	0	5	5
315.0	0	11	11
316.0	0	9	9
317.0	0	6	6
318.0	0	5	5
319.0	0	4	4
321.0	0	5	5
322.0	0	11	11
323.0	0	4	4
324.0	0	3	3
325.0	0	2	2
326.0	0	4	4
327.0	0	8	8
328.0	0	8	8
329.0	0	5	5
330.0	0	10	10
331.0	0	6	6
332.0	0	3	3
333.0	0	4	4
334.0	0	5	5
335.0	0	7	7
336.0	0	2	2
337.0	0	3	3
338.0	0	5	5
339.0	0	5	5
340.0	0	5	5
341.0	0	4	4
342.0	0	2	2
343.0	0	4	4
344.0	0	4	4
345.0	0	8	8
346.0	0	4	4
347.0	0	7	7
348.0	0	3	3
349.0	0	6	6
350.0	0	6	6
351.0	0	3	3
352.0	0	1	1
353.0	0	5	5
354.0	0	3	3
355.0	0	3	3
356.0	0	4	4
357.0	0	2	2
358.0	0	1	1
359.0	0	1	1
360.0	0	4	4
361.0	0	8	8
362.0	0	3	3
363.0	0	3	3
364.0	0	4	4
365.0	0	7	7
366.0	0	3	3
367.0	0	4	4
368.0	0	5	5
369.0	0	7	7
370.0	0	3	3
371.0	0	2	2
372.0	0	3	3
373.0	0	6	6
374.0	0	5	5
375.0	0	4	4
376.0	0	1	1
377.0	0	4	4
378.0	0	2	2
379.0	0	1	1
380.0	0	8	8
381.0	0	2	2
382.0	0	1	1
383.0	0	5	5
384.0	0	2	2
385.0	0	2	2
386.0	0	4	4
387.0	0	5	5
388.0	0	2	2
389.0	0	2	2
390.0	0	3	3
391.0	0	4	4
392.0	0	1	1
393.0	0	2	2
394.0	0	5	5
395.0	0	4	4
396.0	0	7	7
397.0	0	4	4
398.0	0	4	4
399.0	0	4	4
400.0	0	2	2
401.0	0	3	3
402.0	0	4	4
403.0	0	2	2
404.0	0	4	4
405.0	0	5	5
407.0	0	1	1
408.0	0	3	3
409.0	0	2	2
410.0	0	2	2
411.0	0	1	1
412.0	0	1	1
413.0	0	4	4
414.0	0	5	5
415.0	0	3	3
416.0	0	4	4
417.0	0	2	2
418.0	0	1	1
419.0	0	3	3
420.0	0	3	3
421.0	0	2	2
422.0	0	2	2
423.0	0	3	3
424.0	0	2	2
425.0	0	1	1
426.0	0	1	1
427.0	0	1	1
428.0	0	7	7
429.0	0	3	3
430.0	0	1	1
431.0	0	3	3
432.0	0	2	2
433.0	0	1	1
434.0	0	4	4
435.0	0	3	3
436.0	0	3	3
437.0	0	3	3
438.0	0	1	1
439.0	0	6	6
440.0	0	2	2
441.0	0	4	4
442.0	0	1	1
443.0	0	4	4
444.0	0	1	1
445.0	0	4	4
446.0	0	1	1
447.0	0	3	3
448.0	0	1	1
449.0	0	2	2
450.0	0	1	1
451.0	0	3	3
454.0	0	2	2
455.0	0	2	2
456.0	0	4	4
458.0	0	3	3
459.0	0	3	3
460.0	0	2	2
461.0	0	3	3
462.0	0	7	7
463.0	0	2	2
464.0	0	5	5
465.0	0	1	1
466.0	0	1	1
467.0	0	2	2
468.0	0	2	2
469.0	0	1	1
470.0	0	4	4
471.0	0	1	1
472.0	0	3	3
473.0	0	2	2
474.0	0	3	3
476.0	0	1	1
477.0	0	1	1
478.0	0	1	1
479.0	0	4	4
481.0	0	3	3
482.0	0	3	3
483.0	0	2	2
485.0	0	4	4
486.0	0	5	5
487.0	0	1	1
488.0	0	5	5
489.0	0	5	5
490.0	0	1	1
491.0	0	2	2
492.0	0	3	3
493.0	0	3	3
494.0	0	2	2
495.0	0	1	1
496.0	0	1	1
497.0	0	3	3
498.0	0	2	2
499.0	0	4	4
501.0	0	4	4
503.0	0	1	1
504.0	0	2	2
505.0	0	1	1
506.0	0	1	1
507.0	0	2	2
508.0	0	1	1
509.0	0	1	1
510.0	0	1	1
511.0	0	1	1
512.0	0	1	1
513.0	0	2	2
514.0	0	6	6
515.0	0	2	2
517.0	0	2	2
518.0	0	1	1
519.0	0	3	3
520.0	0	2	2
521.0	0	3	3
522.0	0	2	2
523.0	0	3	3
524.0	0	2	2
525.0	0	2	2
526.0	0	1	1
527.0	0	2	2
528.0	0	1	1
529.0	0	4	4
530.0	0	3	3
533.0	0	4	4
535.0	0	2	2
536.0	0	3	3
537.0	0	1	1
538.0	0	2	2
540.0	0	1	1
541.0	0	3	3
542.0	0	2	2
543.0	0	2	2
544.0	0	1	1
545.0	0	2	2
546.0	0	2	2
547.0	0	3	3
548.0	0	1	1
549.0	0	2	2
551.0	0	1	1
552.0	0	2	2
553.0	0	3	3
554.0	0	1	1
557.0	0	2	2
559.0	0	1	1
560.0	0	2	2
561.0	0	4	4
562.0	0	1	1
563.0	0	1	1
564.0	0	1	1
565.0	0	2	2
566.0	0	1	1
567.0	0	1	1
570.0	0	2	2
571.0	0	3	3
572.0	0	1	1
574.0	0	2	2
575.0	0	2	2
578.0	0	3	3
579.0	0	2	2
580.0	0	1	1
581.0	0	4	4
584.0	0	1	1
585.0	0	1	1
587.0	0	1	1
588.0	0	2	2
589.0	0	1	1
590.0	0	1	1
591.0	0	1	1
592.0	0	1	1
593.0	0	3	3
594.0	0	1	1
595.0	0	1	1
599.0	0	1	1
603.0	0	3	3
604.0	0	2	2
605.0	0	4	4
606.0	0	4	4
607.0	0	1	1
608.0	0	2	2
609.0	0	1	1
610.0	0	1	1
613.0	0	1	1
614.0	0	1	1
615.0	0	1	1
616.0	0	1	1
619.0	0	2	2
620.0	0	1	1
623.0	0	1	1
625.0	0	1	1
626.0	0	1	1
628.0	0	2	2
629.0	0	1	1
630.0	0	1	1
632.0	0	1	1
633.0	0	2	2
635.0	0	1	1
636.0	0	2	2
637.0	0	3	3
638.0	0	1	1
642.0	0	1	1
646.0	0	1	1
649.0	0	1	1
650.0	0	1	1
651.0	0	2	2
652.0	0	1	1
653.0	0	1	1
654.0	0	2	2
656.0	0	2	2
657.0	0	1	1
658.0	0	1	1
660.0	0	2	2
662.0	0	1	1
665.0	0	1	1
667.0	0	1	1
669.0	0	2	2
671.0	0	1	1
672.0	0	1	1
675.0	0	1	1
676.0	0	1	1
677.0	0	1	1
678.0	0	1	1
679.0	0	1	1
680.0	0	2	2
683.0	0	2	2
684.0	0	1	1
685.0	0	2	2
688.0	0	3	3
689.0	0	1	1
692.0	0	1	1
694.0	0	1	1
695.0	0	1	1
699.0	0	2	2
701.0	0	1	1
703.0	0	2	2
705.0	0	2	2
706.0	0	1	1
710.0	0	1	1
711.0	0	1	1
713.0	0	1	1
714.0	0	1	1
715.0	0	2	2
716.0	0	2	2
719.0	0	1	1
724.0	0	1	1
725.0	0	1	1
726.0	0	1	1
727.0	0	1	1
728.0	0	1	1
732.0	0	2	2
733.0	0	1	1
736.0	0	5	5
737.0	0	1	1
738.0	0	1	1
740.0	0	1	1
741.0	0	1	1
743.0	0	3	3
744.0	0	1	1
745.0	0	2	2
746.0	0	1	1
750.0	0	1	1
751.0	0	1	1
752.0	0	1	1
753.0	0	1	1
754.0	0	2	2
755.0	0	1	1
757.0	0	3	3
758.0	0	1	1
759.0	0	2	2
763.0	0	1	1
764.0	0	2	2
765.0	0	1	1
767.0	0	1	1
770.0	0	1	1
773.0	0	2	2
774.0	0	1	1
775.0	0	1	1
777.0	0	1	1
778.0	0	1	1
782.0	0	1	1
783.0	0	1	1
785.0	0	2	2
787.0	0	1	1
790.0	0	1	1
791.0	0	3	3
793.0	0	2	2
796.0	0	1	1
800.0	0	2	2
801.0	0	1	1
810.0	0	1	1
811.0	0	1	1
814.0	0	1	1
815.0	0	1	1
816.0	0	1	1
818.0	0	1	1
820.0	0	1	1
825.0	0	2	2
827.0	0	1	1
828.0	0	1	1
829.0	0	3	3
830.0	0	1	1
834.0	0	2	2
835.0	0	2	2
836.0	0	1	1
838.0	0	1	1
839.0	0	2	2
843.0	0	1	1
848.0	0	1	1
853.0	0	1	1
854.0	0	1	1
856.0	0	3	3
857.0	0	1	1
861.0	0	1	1
862.0	0	1	1
863.0	0	3	3
865.0	0	1	1
876.0	0	1	1
882.0	0	1	1
884.0	0	2	2
886.0	0	1	1
895.0	0	2	2
898.0	0	1	1
899.0	0	1	1
903.0	0	1	1
906.0	0	1	1
914.0	0	1	1
918.0	0	1	1
920.0	0	1	1
922.0	0	1	1
924.0	0	1	1
927.0	0	1	1
928.0	0	1	1
930.0	0	1	1
941.0	0	1	1
942.0	0	1	1
956.0	0	1	1
958.0	0	1	1
960.0	0	1	1
963.0	0	2	2
965.0	0	1	1
967.0	0	1	1
969.0	0	1	1
970.0	0	1	1
971.0	0	1	1
978.0	0	1	1
983.0	0	1	1
994.0	0	1	1
997.0	0	2	2
1001.0	0	1	1
1017.0	0	1	1
1027.0	0	1	1
1031.0	0	1	1
1034.0	0	1	1
1038.0	0	1	1
1047.0	0	1	1
1050.0	0	1	1
1051.0	0	1	1
1052.0	0	1	1
1053.0	0	1	1
1063.0	0	1	1
1064.0	0	1	1
1070.0	0	1	1
1079.0	0	1	1
1083.0	0	1	1
1084.0	0	1	1
1099.0	0	1	1
1103.0	0	2	2
1115.0	0	1	1
1125.0	0	1	1
1127.0	0	2	2
1131.0	0	1	1
1133.0	0	1	1
1138.0	0	1	1
1153.0	0	1	1
1157.0	0	1	1
1166.0	0	1	1
1171.0	0	1	1
1172.0	0	1	1
1178.0	0	1	1
1198.0	0	1	1
1201.0	0	1	1
1211.0	0	1	1
1232.0	0	1	1
1248.0	0	1	1
1277.0	0	1	1
1287.0	0	1	1
1333.0	0	2	2
1350.0	0	1	1
1352.0	0	1	1
1353.0	0	1	1
1384.0	0	1	1
1388.0	0	1	1
1391.0	0	1	1
1437.0	0	1	1
1443.0	0	1	1
1445.0	0	1	1
1450.0	0	1	1
1473.0	0	1	1
1492.0	0	1	1
1497.0	0	1	1
1510.0	0	1	1
1514.0	0	1	1
1541.0	0	1	1
1573.0	0	1	1
1601.0	0	1	1
1609.0	0	1	1
1626.0	0	1	1
1638.0	0	1	1
1647.0	0	1	1
1663.0	0	1	1
1672.0	0	1	1
1674.0	0	1	1
1678.0	0	1	1
1741.0	0	1	1
1744.0	0	1	1
1765.0	0	1	1
1782.0	0	1	1
1794.0	0	1	1
1820.0	0	1	1
1843.0	0	1	1
1844.0	0	1	1
1861.0	0	1	1
1990.0	0	1	1
2002.0	0	1	1
2041.0	0	1	1
2140.0	0	1	1
2166.0	0	1	1
2172.0	0	1	1
2189.0	0	1	1
2293.0	0	1	1
2361.0	0	1	1
2526.0	0	1	1
3378.0	0	1	1
4083.0	0	1	1