## 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_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-TA_100nM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-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 21:47:21 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	800331	35836681	0	924253	569078	7550467	0	0.216217	72625560

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24520079	24520079
2.0	1.61052	2848996	2848996
3.0	1.983254	477188	477188
4.0	2.210816	155192	155192
5.0	2.349747	78270	78270
6.0	2.434567	47431	47431
7.0	2.486352	31748	31748
8.0	2.517967	22137	22137
9.0	2.537269	16460	16460
10.0	2.549053	12503	12503
11.0	2.556247	10052	10052
12.0	2.56064	7883	7883
13.0	2.563321	6437	6437
14.0	2.564959	5379	5379
15.0	2.565958	4332	4332
16.0	2.566568	3662	3662
17.0	2.566941	3263	3263
18.0	2.567168	2831	2831
19.0	2.567307	2410	2410
20.0	2.567392	2076	2076
21.0	2.567444	1785	1785
22.0	2.567475	1698	1698
23.0	2.567495	1605	1605
24.0	2.567506	1291	1291
25.0	2.567514	1233	1233
26.0	2.567518	1151	1151
27.0	2.567521	950	950
28.0	2.567522	906	906
29.0	2.567523	869	869
30.0	2.567524	806	806
31.0	2.567524	692	692
32.0	2.567525	684	684
33.0	2.567525	617	617
34.0	2.567525	537	537
35.0	2.567525	509	509
36.0	2.567525	509	509
37.0	2.567525	480	480
38.0	2.567525	448	448
39.0	2.567525	417	417
40.0	2.567525	411	411
41.0	2.567525	348	348
42.0	2.567525	333	333
43.0	2.567525	311	311
44.0	2.567525	287	287
45.0	2.567525	286	286
46.0	2.567525	252	252
47.0	2.567525	294	294
48.0	2.567525	228	228
49.0	2.567525	237	237
50.0	2.567525	249	249
51.0	2.567525	222	222
52.0	2.567525	201	201
53.0	2.567525	177	177
54.0	2.567525	195	195
55.0	2.567525	170	170
56.0	2.567525	151	151
57.0	2.567525	164	164
58.0	2.567525	150	150
59.0	2.567525	151	151
60.0	2.567525	140	140
61.0	2.567525	159	159
62.0	2.567525	144	144
63.0	2.567525	118	118
64.0	2.567525	99	99
65.0	2.567525	100	100
66.0	2.567525	105	105
67.0	2.567525	135	135
68.0	2.567525	93	93
69.0	2.567525	104	104
70.0	2.567525	91	91
71.0	2.567525	97	97
72.0	2.567525	99	99
73.0	2.567525	80	80
74.0	2.567525	73	73
75.0	2.567525	85	85
76.0	2.567525	88	88
77.0	2.567525	69	69
78.0	2.567525	67	67
79.0	2.567525	70	70
80.0	2.567525	71	71
81.0	2.567525	71	71
82.0	2.567525	67	67
83.0	2.567525	71	71
84.0	2.567525	63	63
85.0	2.567525	61	61
86.0	2.567525	61	61
87.0	2.567525	58	58
88.0	2.567525	61	61
89.0	2.567525	50	50
90.0	2.567525	52	52
91.0	2.567525	57	57
92.0	2.567525	44	44
93.0	2.567525	47	47
94.0	2.567525	40	40
95.0	2.567525	50	50
96.0	2.567525	38	38
97.0	2.567525	34	34
98.0	2.567525	51	51
99.0	2.567525	33	33
100.0	2.567525	42	42
101.0	0	45	45
102.0	0	34	34
103.0	0	36	36
104.0	0	35	35
105.0	0	34	34
106.0	0	36	36
107.0	0	23	23
108.0	0	35	35
109.0	0	30	30
110.0	0	33	33
111.0	0	34	34
112.0	0	30	30
113.0	0	36	36
114.0	0	25	25
115.0	0	25	25
116.0	0	28	28
117.0	0	40	40
118.0	0	24	24
119.0	0	22	22
120.0	0	38	38
121.0	0	29	29
122.0	0	27	27
123.0	0	21	21
124.0	0	28	28
125.0	0	24	24
126.0	0	26	26
127.0	0	22	22
128.0	0	22	22
129.0	0	17	17
130.0	0	25	25
131.0	0	22	22
132.0	0	27	27
133.0	0	27	27
134.0	0	24	24
135.0	0	26	26
136.0	0	16	16
137.0	0	26	26
138.0	0	21	21
139.0	0	26	26
140.0	0	14	14
141.0	0	15	15
142.0	0	20	20
143.0	0	19	19
144.0	0	14	14
145.0	0	14	14
146.0	0	11	11
147.0	0	21	21
148.0	0	16	16
149.0	0	20	20
150.0	0	15	15
151.0	0	17	17
152.0	0	15	15
153.0	0	14	14
154.0	0	9	9
155.0	0	14	14
156.0	0	18	18
157.0	0	16	16
158.0	0	13	13
159.0	0	15	15
160.0	0	15	15
161.0	0	15	15
162.0	0	14	14
163.0	0	7	7
164.0	0	14	14
165.0	0	12	12
166.0	0	20	20
167.0	0	14	14
168.0	0	13	13
169.0	0	14	14
170.0	0	12	12
171.0	0	6	6
172.0	0	13	13
173.0	0	11	11
174.0	0	12	12
175.0	0	12	12
176.0	0	12	12
177.0	0	14	14
178.0	0	11	11
179.0	0	14	14
180.0	0	13	13
181.0	0	13	13
182.0	0	6	6
183.0	0	11	11
184.0	0	5	5
185.0	0	8	8
186.0	0	12	12
187.0	0	6	6
188.0	0	10	10
189.0	0	8	8
190.0	0	7	7
191.0	0	5	5
192.0	0	10	10
193.0	0	9	9
194.0	0	10	10
195.0	0	9	9
196.0	0	4	4
197.0	0	7	7
198.0	0	8	8
199.0	0	5	5
200.0	0	7	7
201.0	0	4	4
202.0	0	7	7
203.0	0	8	8
204.0	0	6	6
205.0	0	11	11
206.0	0	6	6
207.0	0	10	10
208.0	0	6	6
209.0	0	5	5
210.0	0	7	7
211.0	0	3	3
212.0	0	5	5
213.0	0	5	5
214.0	0	6	6
215.0	0	7	7
216.0	0	4	4
217.0	0	5	5
218.0	0	7	7
219.0	0	9	9
220.0	0	9	9
221.0	0	7	7
222.0	0	5	5
223.0	0	4	4
224.0	0	9	9
225.0	0	3	3
226.0	0	6	6
227.0	0	7	7
228.0	0	3	3
229.0	0	11	11
230.0	0	7	7
231.0	0	9	9
232.0	0	6	6
233.0	0	6	6
234.0	0	5	5
235.0	0	3	3
236.0	0	5	5
237.0	0	5	5
238.0	0	9	9
239.0	0	7	7
240.0	0	5	5
241.0	0	7	7
242.0	0	2	2
243.0	0	7	7
244.0	0	4	4
245.0	0	3	3
247.0	0	6	6
248.0	0	6	6
249.0	0	6	6
250.0	0	4	4
251.0	0	6	6
252.0	0	2	2
253.0	0	3	3
254.0	0	9	9
255.0	0	4	4
256.0	0	2	2
257.0	0	5	5
258.0	0	2	2
259.0	0	2	2
260.0	0	5	5
261.0	0	1	1
262.0	0	3	3
263.0	0	6	6
264.0	0	5	5
265.0	0	5	5
266.0	0	6	6
267.0	0	1	1
268.0	0	4	4
269.0	0	4	4
270.0	0	1	1
271.0	0	5	5
272.0	0	3	3
273.0	0	2	2
274.0	0	7	7
275.0	0	5	5
276.0	0	4	4
277.0	0	3	3
278.0	0	4	4
279.0	0	6	6
280.0	0	2	2
281.0	0	3	3
282.0	0	2	2
283.0	0	3	3
284.0	0	3	3
285.0	0	2	2
286.0	0	3	3
287.0	0	4	4
288.0	0	1	1
289.0	0	3	3
290.0	0	2	2
291.0	0	9	9
292.0	0	6	6
293.0	0	1	1
294.0	0	4	4
295.0	0	2	2
296.0	0	1	1
297.0	0	5	5
298.0	0	2	2
299.0	0	4	4
300.0	0	1	1
301.0	0	2	2
302.0	0	4	4
303.0	0	5	5
304.0	0	2	2
305.0	0	2	2
306.0	0	2	2
307.0	0	7	7
310.0	0	6	6
311.0	0	1	1
313.0	0	3	3
314.0	0	1	1
315.0	0	1	1
316.0	0	3	3
317.0	0	4	4
318.0	0	3	3
319.0	0	4	4
320.0	0	4	4
321.0	0	2	2
322.0	0	5	5
323.0	0	1	1
324.0	0	1	1
325.0	0	1	1
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	1	1
334.0	0	1	1
335.0	0	5	5
336.0	0	1	1
337.0	0	4	4
339.0	0	1	1
340.0	0	1	1
341.0	0	2	2
342.0	0	2	2
343.0	0	1	1
344.0	0	2	2
345.0	0	1	1
347.0	0	1	1
348.0	0	3	3
349.0	0	1	1
350.0	0	2	2
351.0	0	1	1
353.0	0	2	2
355.0	0	2	2
356.0	0	1	1
357.0	0	4	4
358.0	0	3	3
359.0	0	2	2
360.0	0	2	2
361.0	0	1	1
362.0	0	2	2
363.0	0	1	1
364.0	0	1	1
365.0	0	4	4
369.0	0	3	3
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
373.0	0	1	1
376.0	0	3	3
377.0	0	1	1
378.0	0	5	5
379.0	0	2	2
381.0	0	2	2
382.0	0	1	1
383.0	0	2	2
384.0	0	1	1
385.0	0	1	1
386.0	0	2	2
387.0	0	1	1
388.0	0	1	1
389.0	0	2	2
390.0	0	2	2
391.0	0	1	1
392.0	0	1	1
393.0	0	3	3
394.0	0	2	2
395.0	0	1	1
396.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	2	2
403.0	0	2	2
405.0	0	1	1
408.0	0	2	2
409.0	0	1	1
411.0	0	1	1
412.0	0	1	1
413.0	0	4	4
414.0	0	3	3
416.0	0	1	1
417.0	0	1	1
419.0	0	1	1
421.0	0	1	1
423.0	0	3	3
425.0	0	1	1
426.0	0	2	2
427.0	0	1	1
428.0	0	3	3
430.0	0	1	1
431.0	0	3	3
434.0	0	3	3
436.0	0	1	1
437.0	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	4	4
451.0	0	2	2
453.0	0	2	2
454.0	0	2	2
458.0	0	1	1
461.0	0	1	1
462.0	0	1	1
463.0	0	2	2
464.0	0	1	1
467.0	0	1	1
468.0	0	1	1
471.0	0	1	1
472.0	0	1	1
477.0	0	1	1
478.0	0	1	1
480.0	0	4	4
481.0	0	2	2
483.0	0	2	2
487.0	0	3	3
491.0	0	1	1
492.0	0	1	1
493.0	0	1	1
494.0	0	1	1
498.0	0	2	2
503.0	0	1	1
505.0	0	1	1
506.0	0	1	1
507.0	0	1	1
508.0	0	2	2
510.0	0	2	2
513.0	0	1	1
516.0	0	1	1
517.0	0	1	1
518.0	0	1	1
519.0	0	1	1
522.0	0	2	2
526.0	0	1	1
531.0	0	2	2
533.0	0	1	1
536.0	0	1	1
538.0	0	2	2
539.0	0	2	2
540.0	0	4	4
541.0	0	3	3
543.0	0	1	1
547.0	0	1	1
552.0	0	2	2
554.0	0	2	2
555.0	0	1	1
556.0	0	1	1
558.0	0	1	1
559.0	0	1	1
562.0	0	1	1
563.0	0	2	2
565.0	0	1	1
566.0	0	2	2
570.0	0	1	1
574.0	0	1	1
582.0	0	1	1
585.0	0	1	1
587.0	0	1	1
589.0	0	1	1
593.0	0	1	1
595.0	0	1	1
596.0	0	1	1
598.0	0	2	2
602.0	0	1	1
603.0	0	1	1
604.0	0	2	2
609.0	0	1	1
614.0	0	1	1
619.0	0	1	1
624.0	0	2	2
627.0	0	1	1
631.0	0	1	1
639.0	0	1	1
641.0	0	1	1
646.0	0	1	1
648.0	0	1	1
650.0	0	1	1
653.0	0	1	1
656.0	0	1	1
660.0	0	1	1
663.0	0	1	1
665.0	0	1	1
676.0	0	1	1
677.0	0	1	1
679.0	0	2	2
684.0	0	1	1
687.0	0	1	1
688.0	0	1	1
698.0	0	1	1
705.0	0	2	2
707.0	0	1	1
715.0	0	3	3
716.0	0	1	1
733.0	0	2	2
735.0	0	1	1
738.0	0	1	1
740.0	0	2	2
746.0	0	1	1
754.0	0	1	1
756.0	0	1	1
768.0	0	1	1
771.0	0	1	1
775.0	0	1	1
777.0	0	1	1
778.0	0	1	1
786.0	0	2	2
795.0	0	1	1
797.0	0	1	1
808.0	0	1	1
810.0	0	1	1
812.0	0	1	1
815.0	0	1	1
816.0	0	1	1
820.0	0	1	1
823.0	0	2	2
825.0	0	1	1
830.0	0	1	1
834.0	0	1	1
837.0	0	1	1
839.0	0	1	1
841.0	0	1	1
845.0	0	1	1
868.0	0	1	1
874.0	0	2	2
888.0	0	1	1
900.0	0	1	1
907.0	0	1	1
915.0	0	2	2
918.0	0	1	1
927.0	0	1	1
933.0	0	1	1
938.0	0	1	1
958.0	0	1	1
981.0	0	1	1
986.0	0	1	1
995.0	0	1	1
1012.0	0	1	1
1013.0	0	1	1
1016.0	0	1	1
1019.0	0	1	1
1023.0	0	1	1
1034.0	0	1	1
1041.0	0	1	1
1043.0	0	1	1
1048.0	0	1	1
1065.0	0	1	1
1090.0	0	1	1
1095.0	0	1	1
1116.0	0	1	1
1118.0	0	1	1
1193.0	0	1	1
1226.0	0	1	1
1232.0	0	1	1
1319.0	0	1	1
1326.0	0	1	1
1341.0	0	1	1
1356.0	0	1	1
1358.0	0	1	1
1397.0	0	1	1
1414.0	0	1	1
1426.0	0	1	1
1497.0	0	1	1
1621.0	0	1	1
1715.0	0	1	1