## 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-DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-DMSO_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 18:48:58 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	604819	24193225	0	703985	387331	3573563	0	0.153792	73614445

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	19059428	19059428
2.0	1.719897	1142517	1142517
3.0	2.238148	193211	193211
4.0	2.611235	75794	75794
5.0	2.879819	40455	40455
6.0	3.073171	24484	24484
7.0	3.212365	16238	16238
8.0	3.312571	11715	11715
9.0	3.384708	8648	8648
10.0	3.43664	6457	6457
11.0	3.474025	4908	4908
12.0	3.500938	3986	3986
13.0	3.520313	3304	3304
14.0	3.534261	2575	2575
15.0	3.544302	2274	2274
16.0	3.551531	2038	2038
17.0	3.556735	1736	1736
18.0	3.560481	1483	1483
19.0	3.563178	1278	1278
20.0	3.565119	1122	1122
21.0	3.566517	1030	1030
22.0	3.567523	956	956
23.0	3.568248	801	801
24.0	3.568769	758	758
25.0	3.569144	693	693
26.0	3.569415	620	620
27.0	3.569609	522	522
28.0	3.569749	517	517
29.0	3.56985	441	441
30.0	3.569923	427	427
31.0	3.569975	385	385
32.0	3.570013	349	349
33.0	3.57004	329	329
34.0	3.570059	334	334
35.0	3.570073	274	274
36.0	3.570083	280	280
37.0	3.570091	260	260
38.0	3.570096	258	258
39.0	3.5701	238	238
40.0	3.570102	232	232
41.0	3.570104	224	224
42.0	3.570106	208	208
43.0	3.570107	191	191
44.0	3.570107	178	178
45.0	3.570108	163	163
46.0	3.570108	146	146
47.0	3.570109	111	111
48.0	3.570109	153	153
49.0	3.570109	130	130
50.0	3.570109	122	122
51.0	3.570109	137	137
52.0	3.570109	128	128
53.0	3.570109	121	121
54.0	3.570109	109	109
55.0	3.570109	96	96
56.0	3.570109	105	105
57.0	3.570109	82	82
58.0	3.570109	96	96
59.0	3.570109	73	73
60.0	3.570109	79	79
61.0	3.570109	80	80
62.0	3.570109	80	80
63.0	3.570109	73	73
64.0	3.570109	78	78
65.0	3.570109	88	88
66.0	3.570109	69	69
67.0	3.570109	68	68
68.0	3.570109	65	65
69.0	3.570109	66	66
70.0	3.570109	48	48
71.0	3.570109	53	53
72.0	3.570109	53	53
73.0	3.570109	52	52
74.0	3.570109	47	47
75.0	3.570109	50	50
76.0	3.570109	46	46
77.0	3.570109	55	55
78.0	3.570109	48	48
79.0	3.570109	47	47
80.0	3.570109	44	44
81.0	3.570109	50	50
82.0	3.570109	47	47
83.0	3.570109	35	35
84.0	3.570109	43	43
85.0	3.570109	30	30
86.0	3.570109	26	26
87.0	3.570109	36	36
88.0	3.570109	31	31
89.0	3.570109	37	37
90.0	3.570109	28	28
91.0	3.570109	42	42
92.0	3.570109	30	30
93.0	3.570109	29	29
94.0	3.570109	31	31
95.0	3.570109	33	33
96.0	3.570109	29	29
97.0	3.570109	36	36
98.0	3.570109	26	26
99.0	3.570109	27	27
100.0	3.570109	25	25
101.0	0	18	18
102.0	0	19	19
103.0	0	30	30
104.0	0	23	23
105.0	0	26	26
106.0	0	22	22
107.0	0	25	25
108.0	0	23	23
109.0	0	23	23
110.0	0	23	23
111.0	0	21	21
112.0	0	18	18
113.0	0	24	24
114.0	0	22	22
115.0	0	21	21
116.0	0	13	13
117.0	0	29	29
118.0	0	17	17
119.0	0	17	17
120.0	0	23	23
121.0	0	20	20
122.0	0	14	14
123.0	0	26	26
124.0	0	21	21
125.0	0	14	14
126.0	0	14	14
127.0	0	14	14
128.0	0	15	15
129.0	0	11	11
130.0	0	22	22
131.0	0	11	11
132.0	0	17	17
133.0	0	22	22
134.0	0	13	13
135.0	0	10	10
136.0	0	12	12
137.0	0	5	5
138.0	0	15	15
139.0	0	8	8
140.0	0	13	13
141.0	0	14	14
142.0	0	10	10
143.0	0	18	18
144.0	0	11	11
145.0	0	16	16
146.0	0	11	11
147.0	0	20	20
148.0	0	17	17
149.0	0	14	14
150.0	0	8	8
151.0	0	11	11
152.0	0	9	9
153.0	0	6	6
154.0	0	8	8
155.0	0	5	5
156.0	0	8	8
157.0	0	6	6
158.0	0	12	12
159.0	0	6	6
160.0	0	11	11
161.0	0	10	10
162.0	0	13	13
163.0	0	7	7
164.0	0	6	6
165.0	0	8	8
166.0	0	7	7
167.0	0	11	11
168.0	0	10	10
169.0	0	4	4
170.0	0	6	6
171.0	0	7	7
172.0	0	10	10
173.0	0	2	2
174.0	0	3	3
175.0	0	5	5
176.0	0	11	11
177.0	0	4	4
178.0	0	4	4
179.0	0	7	7
180.0	0	6	6
181.0	0	5	5
182.0	0	4	4
183.0	0	6	6
184.0	0	4	4
185.0	0	6	6
186.0	0	10	10
187.0	0	6	6
188.0	0	5	5
189.0	0	8	8
190.0	0	6	6
191.0	0	6	6
192.0	0	4	4
193.0	0	12	12
194.0	0	7	7
195.0	0	3	3
196.0	0	7	7
197.0	0	5	5
198.0	0	6	6
199.0	0	9	9
200.0	0	5	5
201.0	0	6	6
202.0	0	6	6
203.0	0	6	6
204.0	0	2	2
205.0	0	5	5
206.0	0	5	5
207.0	0	7	7
208.0	0	2	2
209.0	0	5	5
210.0	0	5	5
211.0	0	3	3
212.0	0	3	3
213.0	0	4	4
214.0	0	5	5
215.0	0	7	7
217.0	0	1	1
218.0	0	5	5
219.0	0	4	4
220.0	0	1	1
221.0	0	4	4
222.0	0	7	7
223.0	0	2	2
224.0	0	3	3
225.0	0	3	3
227.0	0	2	2
228.0	0	2	2
229.0	0	2	2
230.0	0	3	3
231.0	0	3	3
232.0	0	4	4
233.0	0	5	5
234.0	0	6	6
235.0	0	2	2
236.0	0	2	2
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
240.0	0	4	4
241.0	0	2	2
242.0	0	2	2
243.0	0	2	2
244.0	0	4	4
245.0	0	3	3
246.0	0	3	3
247.0	0	1	1
248.0	0	1	1
249.0	0	2	2
251.0	0	3	3
252.0	0	4	4
253.0	0	2	2
254.0	0	1	1
255.0	0	3	3
256.0	0	1	1
257.0	0	3	3
258.0	0	2	2
259.0	0	2	2
260.0	0	5	5
262.0	0	1	1
263.0	0	3	3
264.0	0	1	1
265.0	0	3	3
266.0	0	4	4
267.0	0	1	1
268.0	0	2	2
269.0	0	4	4
270.0	0	1	1
271.0	0	1	1
272.0	0	2	2
273.0	0	2	2
274.0	0	3	3
275.0	0	3	3
276.0	0	2	2
277.0	0	2	2
278.0	0	2	2
279.0	0	1	1
280.0	0	2	2
282.0	0	2	2
283.0	0	2	2
285.0	0	4	4
286.0	0	2	2
287.0	0	1	1
288.0	0	3	3
289.0	0	1	1
290.0	0	4	4
291.0	0	1	1
292.0	0	2	2
293.0	0	4	4
294.0	0	3	3
295.0	0	5	5
296.0	0	2	2
297.0	0	2	2
298.0	0	2	2
299.0	0	2	2
300.0	0	3	3
301.0	0	3	3
303.0	0	4	4
304.0	0	2	2
305.0	0	2	2
306.0	0	4	4
307.0	0	5	5
308.0	0	2	2
309.0	0	1	1
310.0	0	2	2
311.0	0	2	2
312.0	0	2	2
315.0	0	1	1
316.0	0	1	1
317.0	0	2	2
319.0	0	2	2
320.0	0	3	3
321.0	0	1	1
323.0	0	2	2
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
328.0	0	3	3
329.0	0	1	1
330.0	0	3	3
331.0	0	1	1
332.0	0	1	1
333.0	0	2	2
337.0	0	1	1
338.0	0	1	1
340.0	0	1	1
342.0	0	2	2
343.0	0	1	1
344.0	0	1	1
345.0	0	1	1
346.0	0	2	2
348.0	0	1	1
350.0	0	2	2
352.0	0	1	1
353.0	0	1	1
355.0	0	2	2
358.0	0	2	2
359.0	0	3	3
360.0	0	1	1
361.0	0	1	1
363.0	0	2	2
364.0	0	1	1
366.0	0	1	1
368.0	0	2	2
370.0	0	3	3
371.0	0	1	1
372.0	0	2	2
373.0	0	1	1
374.0	0	1	1
376.0	0	2	2
377.0	0	2	2
379.0	0	2	2
380.0	0	1	1
384.0	0	1	1
385.0	0	5	5
387.0	0	4	4
388.0	0	4	4
389.0	0	1	1
390.0	0	1	1
391.0	0	2	2
392.0	0	1	1
394.0	0	1	1
396.0	0	2	2
397.0	0	2	2
398.0	0	3	3
399.0	0	2	2
400.0	0	1	1
402.0	0	3	3
403.0	0	1	1
405.0	0	2	2
406.0	0	1	1
407.0	0	1	1
411.0	0	2	2
412.0	0	2	2
418.0	0	1	1
424.0	0	1	1
426.0	0	1	1
429.0	0	1	1
430.0	0	1	1
432.0	0	2	2
434.0	0	1	1
436.0	0	2	2
439.0	0	1	1
442.0	0	1	1
443.0	0	1	1
449.0	0	2	2
450.0	0	1	1
453.0	0	1	1
454.0	0	1	1
460.0	0	1	1
461.0	0	1	1
467.0	0	1	1
469.0	0	1	1
472.0	0	1	1
473.0	0	1	1
474.0	0	1	1
477.0	0	1	1
479.0	0	1	1
481.0	0	2	2
486.0	0	1	1
488.0	0	1	1
489.0	0	2	2
490.0	0	3	3
491.0	0	1	1
492.0	0	1	1
493.0	0	2	2
494.0	0	1	1
496.0	0	2	2
498.0	0	1	1
501.0	0	1	1
503.0	0	2	2
506.0	0	1	1
508.0	0	1	1
513.0	0	2	2
515.0	0	1	1
518.0	0	3	3
519.0	0	1	1
521.0	0	1	1
526.0	0	1	1
529.0	0	2	2
530.0	0	2	2
539.0	0	1	1
540.0	0	2	2
542.0	0	2	2
543.0	0	1	1
545.0	0	1	1
546.0	0	3	3
551.0	0	1	1
558.0	0	1	1
559.0	0	2	2
564.0	0	2	2
566.0	0	2	2
572.0	0	1	1
577.0	0	2	2
578.0	0	1	1
580.0	0	2	2
581.0	0	1	1
585.0	0	1	1
593.0	0	1	1
594.0	0	1	1
599.0	0	1	1
607.0	0	1	1
610.0	0	3	3
611.0	0	1	1
615.0	0	2	2
618.0	0	1	1
630.0	0	1	1
634.0	0	1	1
636.0	0	1	1
643.0	0	1	1
645.0	0	2	2
663.0	0	1	1
664.0	0	1	1
681.0	0	1	1
691.0	0	1	1
735.0	0	1	1
743.0	0	1	1
764.0	0	1	1
779.0	0	1	1
816.0	0	1	1
852.0	0	1	1
860.0	0	1	1
864.0	0	1	1
869.0	0	1	1
874.0	0	1	1
878.0	0	1	1
912.0	0	1	1
919.0	0	1	1
942.0	0	1	1
1000.0	0	1	1
1001.0	0	1	1
1013.0	0	1	1
1016.0	0	1	1
1083.0	0	1	1
1150.0	0	1	1
1162.0	0	1	1
1187.0	0	1	1
1217.0	0	1	1
1259.0	0	1	1
1313.0	0	1	1
1314.0	0	1	1
1323.0	0	1	1
1324.0	0	1	1
1507.0	0	1	1
2101.0	0	1	1