## 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_1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_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 20:24:14 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	1100405	45077200	0	1270721	819483	8926639	0	0.204622	98231907

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32504030	32504030
2.0	1.631988	2554489	2554489
3.0	2.031396	484790	484790
4.0	2.283817	197938	197938
5.0	2.443344	108691	108691
6.0	2.544163	67509	67509
7.0	2.607879	46185	46185
8.0	2.648147	32516	32516
9.0	2.673596	24237	24237
10.0	2.68968	18478	18478
11.0	2.699844	14638	14638
12.0	2.706268	11547	11547
13.0	2.710328	9428	9428
14.0	2.712894	7824	7824
15.0	2.714515	6611	6611
16.0	2.71554	5605	5605
17.0	2.716187	4889	4889
18.0	2.716597	4135	4135
19.0	2.716855	3602	3602
20.0	2.717019	3120	3120
21.0	2.717122	2780	2780
22.0	2.717188	2377	2377
23.0	2.717229	2218	2218
24.0	2.717255	1987	1987
25.0	2.717271	1813	1813
26.0	2.717282	1505	1505
27.0	2.717288	1432	1432
28.0	2.717293	1296	1296
29.0	2.717295	1198	1198
30.0	2.717297	1115	1115
31.0	2.717298	1021	1021
32.0	2.717299	909	909
33.0	2.717299	858	858
34.0	2.717299	882	882
35.0	2.717299	767	767
36.0	2.717299	698	698
37.0	2.7173	683	683
38.0	2.7173	635	635
39.0	2.7173	575	575
40.0	2.7173	574	574
41.0	2.7173	574	574
42.0	2.7173	507	507
43.0	2.7173	433	433
44.0	2.7173	436	436
45.0	2.7173	396	396
46.0	2.7173	360	360
47.0	2.7173	371	371
48.0	2.7173	335	335
49.0	2.7173	335	335
50.0	2.7173	300	300
51.0	2.7173	312	312
52.0	2.7173	308	308
53.0	2.7173	279	279
54.0	2.7173	295	295
55.0	2.7173	254	254
56.0	2.7173	238	238
57.0	2.7173	238	238
58.0	2.7173	202	202
59.0	2.7173	218	218
60.0	2.7173	229	229
61.0	2.7173	203	203
62.0	2.7173	200	200
63.0	2.7173	181	181
64.0	2.7173	171	171
65.0	2.7173	168	168
66.0	2.7173	150	150
67.0	2.7173	190	190
68.0	2.7173	132	132
69.0	2.7173	150	150
70.0	2.7173	140	140
71.0	2.7173	142	142
72.0	2.7173	120	120
73.0	2.7173	116	116
74.0	2.7173	109	109
75.0	2.7173	125	125
76.0	2.7173	119	119
77.0	2.7173	109	109
78.0	2.7173	107	107
79.0	2.7173	116	116
80.0	2.7173	107	107
81.0	2.7173	117	117
82.0	2.7173	90	90
83.0	2.7173	86	86
84.0	2.7173	91	91
85.0	2.7173	94	94
86.0	2.7173	87	87
87.0	2.7173	70	70
88.0	2.7173	71	71
89.0	2.7173	74	74
90.0	2.7173	90	90
91.0	2.7173	78	78
92.0	2.7173	58	58
93.0	2.7173	60	60
94.0	2.7173	88	88
95.0	2.7173	63	63
96.0	2.7173	67	67
97.0	2.7173	59	59
98.0	2.7173	62	62
99.0	2.7173	67	67
100.0	2.7173	46	46
101.0	0	60	60
102.0	0	59	59
103.0	0	62	62
104.0	0	67	67
105.0	0	51	51
106.0	0	50	50
107.0	0	65	65
108.0	0	40	40
109.0	0	50	50
110.0	0	30	30
111.0	0	58	58
112.0	0	45	45
113.0	0	51	51
114.0	0	55	55
115.0	0	27	27
116.0	0	38	38
117.0	0	40	40
118.0	0	37	37
119.0	0	24	24
120.0	0	49	49
121.0	0	32	32
122.0	0	36	36
123.0	0	32	32
124.0	0	37	37
125.0	0	47	47
126.0	0	24	24
127.0	0	38	38
128.0	0	26	26
129.0	0	30	30
130.0	0	30	30
131.0	0	28	28
132.0	0	28	28
133.0	0	32	32
134.0	0	27	27
135.0	0	40	40
136.0	0	23	23
137.0	0	29	29
138.0	0	28	28
139.0	0	31	31
140.0	0	23	23
141.0	0	28	28
142.0	0	26	26
143.0	0	18	18
144.0	0	23	23
145.0	0	23	23
146.0	0	27	27
147.0	0	21	21
148.0	0	23	23
149.0	0	25	25
150.0	0	18	18
151.0	0	18	18
152.0	0	27	27
153.0	0	25	25
154.0	0	15	15
155.0	0	20	20
156.0	0	20	20
157.0	0	19	19
158.0	0	11	11
159.0	0	19	19
160.0	0	15	15
161.0	0	19	19
162.0	0	23	23
163.0	0	14	14
164.0	0	12	12
165.0	0	21	21
166.0	0	21	21
167.0	0	18	18
168.0	0	11	11
169.0	0	16	16
170.0	0	23	23
171.0	0	14	14
172.0	0	24	24
173.0	0	17	17
174.0	0	16	16
175.0	0	13	13
176.0	0	20	20
177.0	0	18	18
178.0	0	12	12
179.0	0	20	20
180.0	0	14	14
181.0	0	16	16
182.0	0	25	25
183.0	0	18	18
184.0	0	11	11
185.0	0	12	12
186.0	0	10	10
187.0	0	13	13
188.0	0	10	10
189.0	0	18	18
190.0	0	13	13
191.0	0	13	13
192.0	0	7	7
193.0	0	10	10
194.0	0	12	12
195.0	0	9	9
196.0	0	12	12
197.0	0	10	10
198.0	0	10	10
199.0	0	10	10
200.0	0	6	6
201.0	0	13	13
202.0	0	8	8
203.0	0	15	15
204.0	0	10	10
205.0	0	10	10
206.0	0	7	7
207.0	0	7	7
208.0	0	15	15
209.0	0	15	15
210.0	0	10	10
211.0	0	5	5
212.0	0	14	14
213.0	0	11	11
214.0	0	9	9
215.0	0	11	11
216.0	0	9	9
217.0	0	10	10
218.0	0	9	9
219.0	0	7	7
220.0	0	9	9
221.0	0	5	5
222.0	0	5	5
223.0	0	8	8
224.0	0	10	10
225.0	0	9	9
226.0	0	12	12
227.0	0	7	7
228.0	0	4	4
229.0	0	5	5
230.0	0	8	8
231.0	0	7	7
232.0	0	8	8
233.0	0	8	8
234.0	0	5	5
235.0	0	6	6
236.0	0	8	8
237.0	0	9	9
238.0	0	4	4
239.0	0	8	8
240.0	0	8	8
241.0	0	5	5
242.0	0	12	12
243.0	0	5	5
244.0	0	4	4
245.0	0	6	6
246.0	0	7	7
247.0	0	5	5
248.0	0	11	11
249.0	0	6	6
250.0	0	12	12
251.0	0	8	8
252.0	0	9	9
253.0	0	11	11
254.0	0	6	6
255.0	0	5	5
256.0	0	4	4
257.0	0	7	7
258.0	0	5	5
259.0	0	4	4
260.0	0	7	7
261.0	0	2	2
262.0	0	5	5
263.0	0	7	7
264.0	0	5	5
265.0	0	4	4
266.0	0	5	5
267.0	0	5	5
268.0	0	6	6
269.0	0	4	4
270.0	0	6	6
272.0	0	6	6
273.0	0	2	2
274.0	0	7	7
275.0	0	5	5
276.0	0	5	5
277.0	0	6	6
278.0	0	4	4
279.0	0	13	13
280.0	0	8	8
281.0	0	9	9
282.0	0	1	1
283.0	0	6	6
284.0	0	5	5
285.0	0	4	4
286.0	0	5	5
287.0	0	7	7
288.0	0	3	3
289.0	0	7	7
290.0	0	4	4
291.0	0	1	1
292.0	0	2	2
293.0	0	3	3
294.0	0	4	4
295.0	0	3	3
296.0	0	7	7
297.0	0	1	1
299.0	0	4	4
300.0	0	3	3
301.0	0	5	5
302.0	0	4	4
303.0	0	4	4
305.0	0	2	2
306.0	0	4	4
307.0	0	2	2
308.0	0	6	6
309.0	0	5	5
310.0	0	2	2
311.0	0	2	2
312.0	0	2	2
313.0	0	3	3
314.0	0	4	4
315.0	0	3	3
316.0	0	7	7
317.0	0	3	3
318.0	0	7	7
319.0	0	3	3
320.0	0	7	7
321.0	0	4	4
322.0	0	2	2
323.0	0	1	1
324.0	0	6	6
325.0	0	1	1
326.0	0	4	4
327.0	0	4	4
328.0	0	1	1
329.0	0	3	3
330.0	0	5	5
331.0	0	3	3
332.0	0	4	4
333.0	0	6	6
334.0	0	2	2
335.0	0	3	3
336.0	0	5	5
337.0	0	5	5
338.0	0	2	2
339.0	0	3	3
340.0	0	2	2
341.0	0	6	6
342.0	0	2	2
343.0	0	2	2
344.0	0	3	3
345.0	0	2	2
346.0	0	4	4
347.0	0	1	1
348.0	0	5	5
349.0	0	4	4
350.0	0	2	2
351.0	0	5	5
352.0	0	3	3
353.0	0	1	1
354.0	0	2	2
355.0	0	2	2
356.0	0	3	3
357.0	0	4	4
358.0	0	2	2
359.0	0	6	6
360.0	0	3	3
361.0	0	4	4
362.0	0	1	1
363.0	0	3	3
364.0	0	3	3
365.0	0	3	3
366.0	0	1	1
367.0	0	4	4
368.0	0	2	2
369.0	0	4	4
370.0	0	3	3
371.0	0	4	4
372.0	0	4	4
373.0	0	1	1
374.0	0	3	3
375.0	0	1	1
377.0	0	3	3
379.0	0	5	5
381.0	0	3	3
382.0	0	1	1
383.0	0	2	2
384.0	0	2	2
385.0	0	4	4
386.0	0	2	2
387.0	0	1	1
388.0	0	3	3
389.0	0	3	3
390.0	0	3	3
391.0	0	2	2
392.0	0	5	5
393.0	0	2	2
394.0	0	2	2
395.0	0	2	2
396.0	0	3	3
397.0	0	2	2
398.0	0	2	2
399.0	0	1	1
400.0	0	3	3
401.0	0	4	4
402.0	0	3	3
403.0	0	3	3
404.0	0	1	1
406.0	0	2	2
407.0	0	7	7
408.0	0	2	2
409.0	0	2	2
410.0	0	3	3
411.0	0	2	2
412.0	0	3	3
413.0	0	5	5
415.0	0	2	2
416.0	0	2	2
417.0	0	1	1
418.0	0	4	4
419.0	0	1	1
421.0	0	3	3
422.0	0	1	1
423.0	0	4	4
424.0	0	2	2
425.0	0	3	3
426.0	0	3	3
427.0	0	4	4
428.0	0	1	1
430.0	0	2	2
432.0	0	2	2
433.0	0	1	1
436.0	0	2	2
438.0	0	3	3
439.0	0	2	2
442.0	0	1	1
443.0	0	1	1
444.0	0	1	1
445.0	0	2	2
446.0	0	3	3
449.0	0	1	1
450.0	0	3	3
451.0	0	2	2
452.0	0	1	1
453.0	0	3	3
454.0	0	1	1
456.0	0	3	3
457.0	0	3	3
458.0	0	2	2
459.0	0	1	1
460.0	0	4	4
461.0	0	1	1
464.0	0	2	2
465.0	0	1	1
467.0	0	2	2
468.0	0	1	1
469.0	0	1	1
470.0	0	2	2
471.0	0	3	3
472.0	0	1	1
474.0	0	1	1
475.0	0	2	2
476.0	0	1	1
477.0	0	2	2
478.0	0	1	1
479.0	0	1	1
480.0	0	2	2
482.0	0	1	1
485.0	0	1	1
486.0	0	2	2
489.0	0	1	1
491.0	0	2	2
493.0	0	2	2
494.0	0	1	1
495.0	0	2	2
496.0	0	3	3
497.0	0	1	1
498.0	0	1	1
500.0	0	1	1
501.0	0	1	1
503.0	0	1	1
505.0	0	4	4
507.0	0	1	1
508.0	0	2	2
509.0	0	1	1
510.0	0	1	1
512.0	0	1	1
515.0	0	1	1
518.0	0	1	1
519.0	0	2	2
520.0	0	1	1
522.0	0	1	1
523.0	0	1	1
526.0	0	2	2
527.0	0	2	2
531.0	0	1	1
532.0	0	1	1
533.0	0	2	2
534.0	0	1	1
537.0	0	1	1
538.0	0	1	1
539.0	0	1	1
540.0	0	1	1
542.0	0	2	2
543.0	0	1	1
547.0	0	1	1
549.0	0	2	2
551.0	0	2	2
555.0	0	1	1
556.0	0	1	1
557.0	0	2	2
558.0	0	2	2
559.0	0	1	1
561.0	0	1	1
562.0	0	1	1
565.0	0	1	1
566.0	0	2	2
567.0	0	1	1
569.0	0	1	1
572.0	0	2	2
576.0	0	1	1
577.0	0	2	2
578.0	0	1	1
583.0	0	1	1
589.0	0	1	1
591.0	0	1	1
595.0	0	3	3
597.0	0	1	1
599.0	0	1	1
601.0	0	1	1
602.0	0	1	1
603.0	0	2	2
607.0	0	1	1
608.0	0	1	1
609.0	0	1	1
610.0	0	1	1
613.0	0	1	1
615.0	0	1	1
617.0	0	2	2
619.0	0	2	2
620.0	0	1	1
621.0	0	1	1
624.0	0	1	1
625.0	0	1	1
626.0	0	1	1
627.0	0	1	1
629.0	0	1	1
631.0	0	1	1
632.0	0	2	2
636.0	0	1	1
638.0	0	1	1
642.0	0	4	4
645.0	0	1	1
648.0	0	1	1
651.0	0	1	1
653.0	0	1	1
662.0	0	1	1
663.0	0	1	1
664.0	0	1	1
667.0	0	1	1
671.0	0	1	1
672.0	0	1	1
674.0	0	1	1
677.0	0	1	1
678.0	0	1	1
680.0	0	1	1
681.0	0	2	2
685.0	0	1	1
687.0	0	2	2
692.0	0	1	1
694.0	0	1	1
696.0	0	2	2
698.0	0	2	2
699.0	0	2	2
700.0	0	1	1
702.0	0	1	1
711.0	0	1	1
724.0	0	1	1
726.0	0	2	2
729.0	0	1	1
739.0	0	2	2
740.0	0	1	1
747.0	0	1	1
748.0	0	2	2
750.0	0	1	1
752.0	0	1	1
753.0	0	1	1
758.0	0	1	1
759.0	0	1	1
766.0	0	1	1
767.0	0	1	1
770.0	0	1	1
773.0	0	1	1
778.0	0	2	2
780.0	0	1	1
782.0	0	1	1
784.0	0	2	2
787.0	0	1	1
790.0	0	1	1
792.0	0	2	2
808.0	0	3	3
809.0	0	1	1
811.0	0	1	1
812.0	0	1	1
815.0	0	2	2
818.0	0	2	2
822.0	0	1	1
827.0	0	1	1
832.0	0	2	2
833.0	0	1	1
840.0	0	2	2
845.0	0	1	1
851.0	0	1	1
858.0	0	2	2
869.0	0	1	1
882.0	0	1	1
886.0	0	1	1
891.0	0	1	1
896.0	0	2	2
905.0	0	1	1
908.0	0	1	1
916.0	0	2	2
923.0	0	1	1
927.0	0	2	2
929.0	0	2	2
930.0	0	1	1
933.0	0	1	1
944.0	0	2	2
945.0	0	1	1
946.0	0	1	1
961.0	0	1	1
963.0	0	1	1
974.0	0	1	1
976.0	0	1	1
977.0	0	1	1
982.0	0	2	2
986.0	0	1	1
1002.0	0	1	1
1004.0	0	1	1
1009.0	0	1	1
1016.0	0	1	1
1031.0	0	1	1
1036.0	0	1	1
1042.0	0	1	1
1050.0	0	1	1
1051.0	0	1	1
1052.0	0	1	1
1059.0	0	1	1
1060.0	0	1	1
1064.0	0	1	1
1067.0	0	1	1
1077.0	0	1	1
1079.0	0	1	1
1083.0	0	1	1
1085.0	0	1	1
1095.0	0	1	1
1129.0	0	1	1
1131.0	0	1	1
1154.0	0	2	2
1156.0	0	1	1
1167.0	0	1	1
1184.0	0	1	1
1188.0	0	1	1
1221.0	0	1	1
1226.0	0	2	2
1231.0	0	1	1
1260.0	0	1	1
1270.0	0	1	1
1273.0	0	1	1
1277.0	0	1	1
1289.0	0	1	1
1309.0	0	1	1
1318.0	0	1	1
1340.0	0	1	1
1351.0	0	1	1
1387.0	0	1	1
1405.0	0	1	1
1443.0	0	1	1
1445.0	0	1	1
1494.0	0	1	1
1552.0	0	1	1
1565.0	0	1	1
1575.0	0	1	1
1590.0	0	1	1
1662.0	0	1	1
1780.0	0	1	1
1972.0	0	1	1
2029.0	0	1	1
2100.0	0	1	1
2250.0	0	1	1
2326.0	0	1	1
2441.0	0	1	1
2494.0	0	1	1
2512.0	0	1	1
2586.0	0	1	1