## 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_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_TA_1uM_2.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 20:06:16 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	1347439	51883909	0	1538295	1041139	10072314	0	0.201548	115709752

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	37133368	37133368
2.0	1.638651	3417244	3417244
3.0	2.046526	603360	603360
4.0	2.307016	223167	223167
5.0	2.473378	118583	118583
6.0	2.579626	73593	73593
7.0	2.647481	48850	48850
8.0	2.690816	34540	34540
9.0	2.718493	25718	25718
10.0	2.736168	19717	19717
11.0	2.747457	15379	15379
12.0	2.754666	12108	12108
13.0	2.759271	9829	9829
14.0	2.762211	8191	8191
15.0	2.764089	6718	6718
16.0	2.765288	5840	5840
17.0	2.766054	4864	4864
18.0	2.766544	4255	4255
19.0	2.766856	3685	3685
20.0	2.767056	3166	3166
21.0	2.767183	2817	2817
22.0	2.767264	2483	2483
23.0	2.767316	2272	2272
24.0	2.76735	2023	2023
25.0	2.767371	1787	1787
26.0	2.767384	1617	1617
27.0	2.767393	1480	1480
28.0	2.767398	1288	1288
29.0	2.767402	1195	1195
30.0	2.767404	1126	1126
31.0	2.767406	1071	1071
32.0	2.767407	921	921
33.0	2.767407	865	865
34.0	2.767408	793	793
35.0	2.767408	805	805
36.0	2.767408	666	666
37.0	2.767408	657	657
38.0	2.767408	567	567
39.0	2.767408	607	607
40.0	2.767408	526	526
41.0	2.767408	510	510
42.0	2.767408	473	473
43.0	2.767408	424	424
44.0	2.767408	446	446
45.0	2.767408	400	400
46.0	2.767408	357	357
47.0	2.767408	348	348
48.0	2.767408	349	349
49.0	2.767408	355	355
50.0	2.767408	325	325
51.0	2.767408	317	317
52.0	2.767408	259	259
53.0	2.767408	266	266
54.0	2.767408	258	258
55.0	2.767408	216	216
56.0	2.767408	248	248
57.0	2.767408	214	214
58.0	2.767408	202	202
59.0	2.767408	187	187
60.0	2.767408	206	206
61.0	2.767408	202	202
62.0	2.767408	165	165
63.0	2.767408	182	182
64.0	2.767408	163	163
65.0	2.767408	156	156
66.0	2.767408	163	163
67.0	2.767408	141	141
68.0	2.767408	141	141
69.0	2.767408	147	147
70.0	2.767408	131	131
71.0	2.767408	146	146
72.0	2.767408	111	111
73.0	2.767408	123	123
74.0	2.767408	126	126
75.0	2.767408	111	111
76.0	2.767408	96	96
77.0	2.767408	97	97
78.0	2.767408	90	90
79.0	2.767408	101	101
80.0	2.767408	82	82
81.0	2.767408	105	105
82.0	2.767408	94	94
83.0	2.767408	91	91
84.0	2.767408	89	89
85.0	2.767408	87	87
86.0	2.767408	96	96
87.0	2.767408	84	84
88.0	2.767408	63	63
89.0	2.767408	68	68
90.0	2.767408	74	74
91.0	2.767408	68	68
92.0	2.767408	63	63
93.0	2.767408	67	67
94.0	2.767408	62	62
95.0	2.767408	60	60
96.0	2.767408	61	61
97.0	2.767408	50	50
98.0	2.767408	75	75
99.0	2.767408	51	51
100.0	2.767408	56	56
101.0	0	37	37
102.0	0	38	38
103.0	0	43	43
104.0	0	51	51
105.0	0	39	39
106.0	0	43	43
107.0	0	42	42
108.0	0	43	43
109.0	0	44	44
110.0	0	35	35
111.0	0	35	35
112.0	0	41	41
113.0	0	39	39
114.0	0	44	44
115.0	0	42	42
116.0	0	30	30
117.0	0	28	28
118.0	0	50	50
119.0	0	29	29
120.0	0	37	37
121.0	0	37	37
122.0	0	29	29
123.0	0	24	24
124.0	0	28	28
125.0	0	32	32
126.0	0	27	27
127.0	0	33	33
128.0	0	24	24
129.0	0	28	28
130.0	0	26	26
131.0	0	36	36
132.0	0	21	21
133.0	0	27	27
134.0	0	33	33
135.0	0	24	24
136.0	0	21	21
137.0	0	26	26
138.0	0	16	16
139.0	0	22	22
140.0	0	21	21
141.0	0	20	20
142.0	0	20	20
143.0	0	27	27
144.0	0	21	21
145.0	0	19	19
146.0	0	24	24
147.0	0	23	23
148.0	0	14	14
149.0	0	13	13
150.0	0	24	24
151.0	0	22	22
152.0	0	22	22
153.0	0	22	22
154.0	0	14	14
155.0	0	23	23
156.0	0	19	19
157.0	0	20	20
158.0	0	8	8
159.0	0	12	12
160.0	0	18	18
161.0	0	17	17
162.0	0	18	18
163.0	0	16	16
164.0	0	10	10
165.0	0	10	10
166.0	0	16	16
167.0	0	22	22
168.0	0	19	19
169.0	0	15	15
170.0	0	13	13
171.0	0	11	11
172.0	0	17	17
173.0	0	17	17
174.0	0	7	7
175.0	0	10	10
176.0	0	13	13
177.0	0	11	11
178.0	0	8	8
179.0	0	14	14
180.0	0	13	13
181.0	0	9	9
182.0	0	11	11
183.0	0	10	10
184.0	0	11	11
185.0	0	13	13
186.0	0	11	11
187.0	0	9	9
188.0	0	9	9
189.0	0	6	6
190.0	0	8	8
191.0	0	11	11
192.0	0	14	14
193.0	0	14	14
194.0	0	11	11
195.0	0	14	14
196.0	0	12	12
197.0	0	12	12
198.0	0	4	4
199.0	0	9	9
200.0	0	8	8
201.0	0	5	5
202.0	0	6	6
203.0	0	13	13
204.0	0	7	7
205.0	0	6	6
206.0	0	10	10
207.0	0	7	7
208.0	0	16	16
209.0	0	8	8
210.0	0	6	6
211.0	0	10	10
212.0	0	8	8
213.0	0	13	13
214.0	0	9	9
215.0	0	7	7
216.0	0	11	11
217.0	0	10	10
218.0	0	2	2
219.0	0	6	6
220.0	0	9	9
221.0	0	7	7
222.0	0	8	8
223.0	0	10	10
224.0	0	3	3
225.0	0	2	2
226.0	0	6	6
227.0	0	8	8
228.0	0	13	13
229.0	0	7	7
230.0	0	6	6
231.0	0	6	6
232.0	0	13	13
233.0	0	8	8
234.0	0	4	4
235.0	0	9	9
236.0	0	5	5
237.0	0	7	7
238.0	0	5	5
239.0	0	7	7
240.0	0	10	10
241.0	0	10	10
242.0	0	8	8
243.0	0	4	4
244.0	0	2	2
245.0	0	9	9
246.0	0	7	7
247.0	0	7	7
248.0	0	6	6
249.0	0	6	6
250.0	0	5	5
251.0	0	7	7
252.0	0	3	3
253.0	0	7	7
254.0	0	3	3
255.0	0	6	6
256.0	0	5	5
257.0	0	10	10
258.0	0	6	6
259.0	0	5	5
260.0	0	4	4
261.0	0	7	7
262.0	0	7	7
263.0	0	5	5
264.0	0	3	3
265.0	0	5	5
266.0	0	5	5
267.0	0	8	8
268.0	0	6	6
269.0	0	7	7
270.0	0	5	5
271.0	0	6	6
272.0	0	4	4
273.0	0	5	5
274.0	0	4	4
275.0	0	5	5
276.0	0	2	2
277.0	0	3	3
278.0	0	2	2
279.0	0	5	5
280.0	0	4	4
281.0	0	2	2
282.0	0	11	11
283.0	0	3	3
284.0	0	5	5
285.0	0	5	5
286.0	0	4	4
287.0	0	3	3
288.0	0	4	4
289.0	0	4	4
290.0	0	5	5
291.0	0	5	5
292.0	0	3	3
293.0	0	3	3
294.0	0	1	1
295.0	0	7	7
296.0	0	3	3
297.0	0	2	2
298.0	0	10	10
299.0	0	3	3
300.0	0	5	5
302.0	0	5	5
304.0	0	2	2
305.0	0	3	3
306.0	0	4	4
307.0	0	1	1
308.0	0	1	1
309.0	0	1	1
310.0	0	2	2
311.0	0	2	2
312.0	0	3	3
313.0	0	3	3
314.0	0	4	4
315.0	0	5	5
316.0	0	6	6
317.0	0	2	2
318.0	0	1	1
319.0	0	1	1
320.0	0	4	4
321.0	0	2	2
322.0	0	1	1
324.0	0	3	3
325.0	0	7	7
326.0	0	2	2
327.0	0	4	4
328.0	0	4	4
329.0	0	3	3
330.0	0	3	3
331.0	0	2	2
332.0	0	5	5
333.0	0	1	1
334.0	0	4	4
335.0	0	3	3
336.0	0	5	5
337.0	0	3	3
338.0	0	1	1
341.0	0	1	1
342.0	0	1	1
343.0	0	1	1
344.0	0	3	3
345.0	0	2	2
346.0	0	4	4
347.0	0	3	3
348.0	0	2	2
349.0	0	3	3
350.0	0	2	2
351.0	0	2	2
352.0	0	4	4
353.0	0	1	1
354.0	0	2	2
355.0	0	2	2
356.0	0	4	4
357.0	0	1	1
358.0	0	1	1
359.0	0	2	2
360.0	0	5	5
361.0	0	5	5
362.0	0	4	4
363.0	0	3	3
366.0	0	1	1
367.0	0	4	4
368.0	0	1	1
369.0	0	2	2
370.0	0	3	3
371.0	0	1	1
372.0	0	2	2
374.0	0	1	1
375.0	0	6	6
376.0	0	1	1
377.0	0	2	2
378.0	0	1	1
379.0	0	1	1
380.0	0	2	2
382.0	0	3	3
383.0	0	3	3
384.0	0	4	4
385.0	0	4	4
386.0	0	1	1
387.0	0	4	4
389.0	0	1	1
390.0	0	2	2
391.0	0	3	3
392.0	0	2	2
393.0	0	3	3
394.0	0	1	1
395.0	0	2	2
396.0	0	2	2
397.0	0	1	1
399.0	0	2	2
400.0	0	3	3
401.0	0	2	2
405.0	0	1	1
407.0	0	1	1
410.0	0	1	1
411.0	0	1	1
414.0	0	2	2
415.0	0	4	4
416.0	0	2	2
417.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	1	1
422.0	0	2	2
423.0	0	2	2
424.0	0	3	3
425.0	0	1	1
426.0	0	3	3
431.0	0	2	2
435.0	0	1	1
436.0	0	1	1
437.0	0	2	2
438.0	0	1	1
439.0	0	2	2
440.0	0	3	3
442.0	0	1	1
445.0	0	1	1
446.0	0	1	1
447.0	0	1	1
448.0	0	1	1
449.0	0	2	2
450.0	0	3	3
451.0	0	2	2
452.0	0	1	1
455.0	0	4	4
456.0	0	1	1
457.0	0	1	1
459.0	0	1	1
460.0	0	1	1
462.0	0	2	2
464.0	0	2	2
466.0	0	1	1
468.0	0	1	1
471.0	0	1	1
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
476.0	0	2	2
477.0	0	1	1
478.0	0	1	1
479.0	0	1	1
480.0	0	3	3
482.0	0	1	1
486.0	0	1	1
487.0	0	2	2
488.0	0	2	2
489.0	0	4	4
490.0	0	3	3
492.0	0	1	1
493.0	0	1	1
494.0	0	1	1
495.0	0	2	2
496.0	0	2	2
497.0	0	1	1
498.0	0	1	1
501.0	0	1	1
503.0	0	2	2
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	2	2
517.0	0	1	1
525.0	0	2	2
528.0	0	1	1
529.0	0	1	1
532.0	0	5	5
535.0	0	2	2
536.0	0	1	1
538.0	0	2	2
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
544.0	0	1	1
545.0	0	2	2
547.0	0	2	2
548.0	0	2	2
551.0	0	1	1
556.0	0	1	1
568.0	0	1	1
570.0	0	1	1
571.0	0	1	1
574.0	0	2	2
578.0	0	1	1
581.0	0	1	1
582.0	0	2	2
584.0	0	3	3
585.0	0	2	2
588.0	0	1	1
589.0	0	1	1
591.0	0	2	2
596.0	0	3	3
601.0	0	2	2
604.0	0	1	1
605.0	0	1	1
608.0	0	1	1
625.0	0	1	1
626.0	0	1	1
627.0	0	1	1
630.0	0	1	1
631.0	0	1	1
632.0	0	1	1
634.0	0	1	1
636.0	0	1	1
640.0	0	1	1
644.0	0	1	1
646.0	0	1	1
647.0	0	1	1
648.0	0	1	1
651.0	0	1	1
653.0	0	2	2
656.0	0	1	1
657.0	0	1	1
658.0	0	3	3
667.0	0	1	1
668.0	0	2	2
669.0	0	2	2
670.0	0	1	1
676.0	0	1	1
681.0	0	1	1
682.0	0	1	1
689.0	0	1	1
693.0	0	2	2
694.0	0	1	1
703.0	0	2	2
708.0	0	1	1
713.0	0	1	1
715.0	0	1	1
718.0	0	1	1
721.0	0	1	1
730.0	0	2	2
734.0	0	1	1
735.0	0	1	1
740.0	0	2	2
743.0	0	1	1
744.0	0	1	1
746.0	0	1	1
750.0	0	1	1
751.0	0	1	1
754.0	0	2	2
756.0	0	1	1
762.0	0	1	1
766.0	0	2	2
768.0	0	1	1
769.0	0	2	2
772.0	0	1	1
779.0	0	1	1
782.0	0	1	1
783.0	0	1	1
784.0	0	2	2
786.0	0	1	1
787.0	0	1	1
800.0	0	1	1
802.0	0	1	1
805.0	0	1	1
807.0	0	1	1
808.0	0	3	3
811.0	0	1	1
817.0	0	1	1
822.0	0	1	1
833.0	0	1	1
837.0	0	1	1
843.0	0	1	1
848.0	0	2	2
857.0	0	1	1
864.0	0	1	1
870.0	0	1	1
874.0	0	1	1
890.0	0	1	1
894.0	0	1	1
906.0	0	1	1
907.0	0	1	1
913.0	0	1	1
916.0	0	1	1
933.0	0	1	1
934.0	0	1	1
948.0	0	1	1
953.0	0	1	1
962.0	0	1	1
971.0	0	1	1
976.0	0	2	2
978.0	0	1	1
979.0	0	1	1
983.0	0	1	1
987.0	0	1	1
993.0	0	1	1
1026.0	0	1	1
1029.0	0	1	1
1030.0	0	1	1
1058.0	0	1	1
1059.0	0	1	1
1069.0	0	1	1
1081.0	0	1	1
1084.0	0	1	1
1086.0	0	1	1
1090.0	0	1	1
1092.0	0	1	1
1123.0	0	1	1
1151.0	0	1	1
1170.0	0	1	1
1174.0	0	1	1
1200.0	0	1	1
1243.0	0	1	1
1276.0	0	1	1
1305.0	0	1	1
1323.0	0	1	1
1330.0	0	1	1
1334.0	0	1	1
1339.0	0	1	1
1512.0	0	1	1
1556.0	0	1	1
1629.0	0	1	1
1737.0	0	1	1
1901.0	0	1	1
1921.0	0	1	1
1962.0	0	1	1
1986.0	0	1	1
2041.0	0	1	1
2123.0	0	1	1
2154.0	0	1	1
2157.0	0	1	1
2173.0	0	1	1
2225.0	0	1	1
2607.0	0	1	1
2750.0	0	1	1