## 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_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_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 18:17:20 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	846070	35824201	0	1363722	621974	7372800	0	0.211983	74631082

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25538113	25538113
2.0	1.618773	1926471	1926471
3.0	2.001653	422259	422259
4.0	2.238568	183142	183142
5.0	2.385165	101681	101681
6.0	2.475875	64560	64560
7.0	2.532004	43284	43284
8.0	2.566735	31060	31060
9.0	2.588226	22730	22730
10.0	2.601524	17284	17284
11.0	2.609752	13679	13679
12.0	2.614843	10977	10977
13.0	2.617994	8913	8913
14.0	2.619943	7462	7462
15.0	2.62115	6304	6304
16.0	2.621896	5185	5185
17.0	2.622358	4400	4400
18.0	2.622644	3874	3874
19.0	2.62282	3306	3306
20.0	2.62293	2974	2974
21.0	2.622998	2587	2587
22.0	2.623039	2213	2213
23.0	2.623065	1979	1979
24.0	2.623081	1784	1784
25.0	2.623091	1593	1593
26.0	2.623097	1479	1479
27.0	2.623101	1332	1332
28.0	2.623104	1148	1148
29.0	2.623105	1090	1090
30.0	2.623106	1006	1006
31.0	2.623107	891	891
32.0	2.623107	814	814
33.0	2.623107	753	753
34.0	2.623107	695	695
35.0	2.623107	650	650
36.0	2.623107	617	617
37.0	2.623107	547	547
38.0	2.623107	500	500
39.0	2.623107	500	500
40.0	2.623107	453	453
41.0	2.623107	433	433
42.0	2.623107	409	409
43.0	2.623107	389	389
44.0	2.623107	368	368
45.0	2.623107	330	330
46.0	2.623107	323	323
47.0	2.623107	302	302
48.0	2.623107	250	250
49.0	2.623107	256	256
50.0	2.623107	288	288
51.0	2.623107	240	240
52.0	2.623107	207	207
53.0	2.623107	233	233
54.0	2.623107	233	233
55.0	2.623107	192	192
56.0	2.623107	199	199
57.0	2.623107	174	174
58.0	2.623107	161	161
59.0	2.623107	183	183
60.0	2.623107	165	165
61.0	2.623107	129	129
62.0	2.623107	145	145
63.0	2.623107	132	132
64.0	2.623107	147	147
65.0	2.623107	139	139
66.0	2.623107	140	140
67.0	2.623107	109	109
68.0	2.623107	109	109
69.0	2.623107	103	103
70.0	2.623107	97	97
71.0	2.623107	133	133
72.0	2.623107	99	99
73.0	2.623107	96	96
74.0	2.623107	107	107
75.0	2.623107	92	92
76.0	2.623107	99	99
77.0	2.623107	90	90
78.0	2.623107	68	68
79.0	2.623107	79	79
80.0	2.623107	96	96
81.0	2.623107	74	74
82.0	2.623107	77	77
83.0	2.623107	69	69
84.0	2.623107	64	64
85.0	2.623107	55	55
86.0	2.623107	53	53
87.0	2.623107	46	46
88.0	2.623107	58	58
89.0	2.623107	56	56
90.0	2.623107	60	60
91.0	2.623107	49	49
92.0	2.623107	56	56
93.0	2.623107	44	44
94.0	2.623107	54	54
95.0	2.623107	55	55
96.0	2.623107	51	51
97.0	2.623107	48	48
98.0	2.623107	44	44
99.0	2.623107	38	38
100.0	2.623107	49	49
101.0	0	32	32
102.0	0	47	47
103.0	0	38	38
104.0	0	26	26
105.0	0	28	28
106.0	0	28	28
107.0	0	28	28
108.0	0	22	22
109.0	0	25	25
110.0	0	27	27
111.0	0	43	43
112.0	0	36	36
113.0	0	32	32
114.0	0	29	29
115.0	0	27	27
116.0	0	32	32
117.0	0	23	23
118.0	0	22	22
119.0	0	17	17
120.0	0	28	28
121.0	0	31	31
122.0	0	26	26
123.0	0	15	15
124.0	0	18	18
125.0	0	19	19
126.0	0	29	29
127.0	0	27	27
128.0	0	16	16
129.0	0	24	24
130.0	0	35	35
131.0	0	28	28
132.0	0	28	28
133.0	0	16	16
134.0	0	23	23
135.0	0	16	16
136.0	0	22	22
137.0	0	19	19
138.0	0	32	32
139.0	0	17	17
140.0	0	15	15
141.0	0	16	16
142.0	0	18	18
143.0	0	18	18
144.0	0	17	17
145.0	0	10	10
146.0	0	14	14
147.0	0	15	15
148.0	0	15	15
149.0	0	16	16
150.0	0	10	10
151.0	0	10	10
152.0	0	12	12
153.0	0	12	12
154.0	0	10	10
155.0	0	15	15
156.0	0	19	19
157.0	0	12	12
158.0	0	19	19
159.0	0	6	6
160.0	0	16	16
161.0	0	8	8
162.0	0	13	13
163.0	0	9	9
164.0	0	16	16
165.0	0	16	16
166.0	0	12	12
167.0	0	9	9
168.0	0	14	14
169.0	0	6	6
170.0	0	11	11
171.0	0	15	15
172.0	0	6	6
173.0	0	13	13
174.0	0	10	10
175.0	0	13	13
176.0	0	7	7
177.0	0	11	11
178.0	0	13	13
179.0	0	11	11
180.0	0	4	4
181.0	0	7	7
182.0	0	10	10
183.0	0	7	7
184.0	0	14	14
185.0	0	9	9
186.0	0	4	4
187.0	0	10	10
188.0	0	7	7
189.0	0	7	7
190.0	0	7	7
191.0	0	6	6
192.0	0	6	6
193.0	0	12	12
194.0	0	11	11
195.0	0	6	6
196.0	0	13	13
197.0	0	4	4
198.0	0	5	5
199.0	0	5	5
200.0	0	7	7
201.0	0	5	5
202.0	0	14	14
203.0	0	11	11
204.0	0	8	8
205.0	0	5	5
206.0	0	4	4
207.0	0	6	6
208.0	0	5	5
209.0	0	7	7
210.0	0	3	3
211.0	0	7	7
212.0	0	5	5
213.0	0	4	4
214.0	0	6	6
215.0	0	2	2
216.0	0	5	5
217.0	0	2	2
218.0	0	7	7
219.0	0	4	4
220.0	0	4	4
221.0	0	8	8
222.0	0	9	9
223.0	0	2	2
224.0	0	5	5
225.0	0	5	5
226.0	0	2	2
227.0	0	2	2
228.0	0	2	2
229.0	0	7	7
230.0	0	7	7
231.0	0	4	4
232.0	0	5	5
233.0	0	8	8
234.0	0	4	4
235.0	0	7	7
236.0	0	6	6
237.0	0	2	2
238.0	0	4	4
239.0	0	4	4
240.0	0	4	4
241.0	0	2	2
242.0	0	8	8
243.0	0	5	5
244.0	0	3	3
245.0	0	2	2
246.0	0	4	4
247.0	0	2	2
248.0	0	8	8
249.0	0	6	6
250.0	0	5	5
251.0	0	3	3
252.0	0	5	5
253.0	0	4	4
254.0	0	2	2
255.0	0	1	1
256.0	0	5	5
257.0	0	4	4
258.0	0	5	5
259.0	0	3	3
260.0	0	5	5
261.0	0	5	5
262.0	0	3	3
263.0	0	1	1
264.0	0	2	2
265.0	0	6	6
266.0	0	5	5
267.0	0	1	1
268.0	0	5	5
269.0	0	5	5
270.0	0	1	1
271.0	0	2	2
272.0	0	4	4
273.0	0	3	3
275.0	0	1	1
276.0	0	4	4
277.0	0	2	2
278.0	0	2	2
279.0	0	4	4
280.0	0	1	1
281.0	0	1	1
282.0	0	6	6
283.0	0	1	1
284.0	0	1	1
285.0	0	1	1
286.0	0	4	4
287.0	0	2	2
288.0	0	4	4
289.0	0	2	2
290.0	0	2	2
291.0	0	1	1
292.0	0	3	3
293.0	0	3	3
294.0	0	1	1
295.0	0	4	4
296.0	0	2	2
297.0	0	2	2
298.0	0	2	2
300.0	0	5	5
301.0	0	2	2
302.0	0	1	1
303.0	0	3	3
304.0	0	2	2
305.0	0	3	3
306.0	0	1	1
307.0	0	1	1
308.0	0	5	5
309.0	0	4	4
311.0	0	1	1
312.0	0	1	1
313.0	0	4	4
314.0	0	2	2
315.0	0	1	1
316.0	0	3	3
317.0	0	5	5
318.0	0	1	1
320.0	0	6	6
321.0	0	3	3
322.0	0	3	3
323.0	0	2	2
324.0	0	7	7
325.0	0	2	2
326.0	0	3	3
327.0	0	4	4
328.0	0	4	4
330.0	0	2	2
331.0	0	3	3
332.0	0	4	4
333.0	0	2	2
334.0	0	1	1
335.0	0	4	4
336.0	0	3	3
337.0	0	2	2
338.0	0	2	2
339.0	0	3	3
340.0	0	1	1
341.0	0	1	1
343.0	0	2	2
344.0	0	1	1
349.0	0	3	3
350.0	0	2	2
351.0	0	3	3
352.0	0	1	1
353.0	0	1	1
354.0	0	2	2
355.0	0	1	1
358.0	0	1	1
359.0	0	1	1
360.0	0	3	3
363.0	0	2	2
365.0	0	1	1
366.0	0	4	4
368.0	0	2	2
369.0	0	2	2
370.0	0	2	2
371.0	0	2	2
372.0	0	3	3
373.0	0	4	4
376.0	0	1	1
377.0	0	2	2
378.0	0	3	3
379.0	0	3	3
380.0	0	1	1
381.0	0	1	1
382.0	0	1	1
383.0	0	1	1
384.0	0	2	2
385.0	0	1	1
386.0	0	1	1
387.0	0	3	3
390.0	0	1	1
391.0	0	1	1
393.0	0	1	1
394.0	0	3	3
396.0	0	1	1
397.0	0	1	1
399.0	0	1	1
401.0	0	2	2
403.0	0	1	1
404.0	0	3	3
405.0	0	1	1
406.0	0	1	1
407.0	0	1	1
409.0	0	3	3
410.0	0	1	1
411.0	0	1	1
412.0	0	1	1
418.0	0	1	1
420.0	0	1	1
422.0	0	2	2
423.0	0	3	3
424.0	0	1	1
425.0	0	1	1
429.0	0	1	1
438.0	0	1	1
443.0	0	3	3
444.0	0	3	3
448.0	0	2	2
451.0	0	3	3
452.0	0	1	1
453.0	0	2	2
455.0	0	1	1
457.0	0	1	1
459.0	0	2	2
462.0	0	3	3
464.0	0	1	1
468.0	0	2	2
474.0	0	1	1
477.0	0	3	3
478.0	0	2	2
482.0	0	1	1
483.0	0	1	1
485.0	0	1	1
491.0	0	1	1
494.0	0	1	1
495.0	0	1	1
497.0	0	1	1
499.0	0	1	1
500.0	0	1	1
502.0	0	2	2
508.0	0	1	1
510.0	0	1	1
514.0	0	1	1
515.0	0	1	1
516.0	0	1	1
519.0	0	1	1
521.0	0	1	1
522.0	0	1	1
525.0	0	1	1
527.0	0	1	1
528.0	0	1	1
529.0	0	1	1
531.0	0	2	2
533.0	0	1	1
535.0	0	1	1
538.0	0	2	2
539.0	0	1	1
540.0	0	1	1
543.0	0	1	1
544.0	0	1	1
548.0	0	1	1
549.0	0	1	1
555.0	0	1	1
559.0	0	1	1
560.0	0	1	1
562.0	0	1	1
565.0	0	1	1
571.0	0	2	2
579.0	0	1	1
582.0	0	2	2
585.0	0	1	1
587.0	0	1	1
589.0	0	1	1
592.0	0	1	1
594.0	0	2	2
601.0	0	1	1
604.0	0	1	1
605.0	0	1	1
610.0	0	1	1
612.0	0	1	1
622.0	0	1	1
623.0	0	1	1
652.0	0	1	1
653.0	0	2	2
654.0	0	1	1
658.0	0	1	1
659.0	0	1	1
663.0	0	1	1
666.0	0	1	1
669.0	0	1	1
673.0	0	1	1
674.0	0	1	1
683.0	0	1	1
688.0	0	1	1
691.0	0	1	1
694.0	0	1	1
702.0	0	1	1
711.0	0	1	1
714.0	0	1	1
718.0	0	1	1
722.0	0	1	1
732.0	0	1	1
737.0	0	1	1
753.0	0	1	1
761.0	0	1	1
763.0	0	1	1
771.0	0	1	1
790.0	0	1	1
803.0	0	1	1
815.0	0	1	1
821.0	0	1	1
823.0	0	1	1
826.0	0	1	1
829.0	0	1	1
838.0	0	1	1
840.0	0	1	1
844.0	0	1	1
846.0	0	2	2
850.0	0	1	1
857.0	0	1	1
864.0	0	1	1
870.0	0	1	1
872.0	0	1	1
885.0	0	1	1
892.0	0	1	1
897.0	0	1	1
898.0	0	1	1
908.0	0	1	1
920.0	0	1	1
930.0	0	1	1
938.0	0	1	1
995.0	0	1	1
1038.0	0	1	1
1065.0	0	1	1
1072.0	0	1	1
1077.0	0	1	1
1084.0	0	1	1
1112.0	0	1	1
1144.0	0	1	1
1145.0	0	1	1
1170.0	0	1	1
1172.0	0	1	1
1222.0	0	1	1
1285.0	0	1	1
1290.0	0	1	1
1313.0	0	1	1
1330.0	0	1	1
1332.0	0	2	2
1333.0	0	1	1
1345.0	0	1	1
1348.0	0	1	1
1350.0	0	1	1
1363.0	0	1	1
1372.0	0	1	1
1383.0	0	1	1
1400.0	0	1	1
1555.0	0	1	1
1569.0	0	1	1
1626.0	0	1	1
1733.0	0	1	1
1761.0	0	1	1
2109.0	0	1	1