## 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_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_1uM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_TA_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 21:19:24 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	1088665	40699173	0	1239761	798501	7193031	0	0.184084	101132018

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	29946931	29946931
2.0	1.668689	2638798	2638798
3.0	2.115834	451058	451058
4.0	2.414835	164187	164187
5.0	2.614774	85963	85963
6.0	2.748471	52585	52585
7.0	2.837872	34644	34644
8.0	2.897654	24197	24197
9.0	2.93763	18006	18006
10.0	2.964361	13647	13647
11.0	2.982236	10527	10527
12.0	2.994189	8274	8274
13.0	3.002181	6796	6796
14.0	3.007526	5667	5667
15.0	3.0111	4666	4666
16.0	3.013489	3941	3941
17.0	3.015087	3316	3316
18.0	3.016156	2870	2870
19.0	3.016871	2463	2463
20.0	3.017348	2179	2179
21.0	3.017668	1882	1882
22.0	3.017882	1647	1647
23.0	3.018024	1443	1443
24.0	3.01812	1329	1329
25.0	3.018184	1197	1197
26.0	3.018227	1070	1070
27.0	3.018255	962	962
28.0	3.018274	862	862
29.0	3.018287	841	841
30.0	3.018296	746	746
31.0	3.018301	697	697
32.0	3.018305	633	633
33.0	3.018308	614	614
34.0	3.018309	534	534
35.0	3.018311	509	509
36.0	3.018311	471	471
37.0	3.018312	427	427
38.0	3.018312	384	384
39.0	3.018312	355	355
40.0	3.018313	352	352
41.0	3.018313	303	303
42.0	3.018313	339	339
43.0	3.018313	278	278
44.0	3.018313	253	253
45.0	3.018313	253	253
46.0	3.018313	258	258
47.0	3.018313	228	228
48.0	3.018313	229	229
49.0	3.018313	196	196
50.0	3.018313	190	190
51.0	3.018313	188	188
52.0	3.018313	178	178
53.0	3.018313	167	167
54.0	3.018313	149	149
55.0	3.018313	148	148
56.0	3.018313	135	135
57.0	3.018313	135	135
58.0	3.018313	124	124
59.0	3.018313	141	141
60.0	3.018313	112	112
61.0	3.018313	124	124
62.0	3.018313	124	124
63.0	3.018313	117	117
64.0	3.018313	119	119
65.0	3.018313	84	84
66.0	3.018313	75	75
67.0	3.018313	100	100
68.0	3.018313	91	91
69.0	3.018313	71	71
70.0	3.018313	92	92
71.0	3.018313	86	86
72.0	3.018313	73	73
73.0	3.018313	79	79
74.0	3.018313	65	65
75.0	3.018313	61	61
76.0	3.018313	63	63
77.0	3.018313	56	56
78.0	3.018313	45	45
79.0	3.018313	65	65
80.0	3.018313	68	68
81.0	3.018313	54	54
82.0	3.018313	45	45
83.0	3.018313	42	42
84.0	3.018313	52	52
85.0	3.018313	47	47
86.0	3.018313	53	53
87.0	3.018313	43	43
88.0	3.018313	41	41
89.0	3.018313	43	43
90.0	3.018313	39	39
91.0	3.018313	39	39
92.0	3.018313	35	35
93.0	3.018313	36	36
94.0	3.018313	44	44
95.0	3.018313	39	39
96.0	3.018313	36	36
97.0	3.018313	42	42
98.0	3.018313	28	28
99.0	3.018313	42	42
100.0	3.018313	33	33
101.0	0	43	43
102.0	0	30	30
103.0	0	29	29
104.0	0	23	23
105.0	0	23	23
106.0	0	22	22
107.0	0	24	24
108.0	0	25	25
109.0	0	36	36
110.0	0	22	22
111.0	0	24	24
112.0	0	9	9
113.0	0	17	17
114.0	0	29	29
115.0	0	27	27
116.0	0	22	22
117.0	0	25	25
118.0	0	17	17
119.0	0	27	27
120.0	0	26	26
121.0	0	17	17
122.0	0	21	21
123.0	0	18	18
124.0	0	20	20
125.0	0	14	14
126.0	0	14	14
127.0	0	15	15
128.0	0	14	14
129.0	0	20	20
130.0	0	15	15
131.0	0	27	27
132.0	0	15	15
133.0	0	15	15
134.0	0	18	18
135.0	0	17	17
136.0	0	10	10
137.0	0	11	11
138.0	0	15	15
139.0	0	24	24
140.0	0	12	12
141.0	0	17	17
142.0	0	6	6
143.0	0	20	20
144.0	0	19	19
145.0	0	13	13
146.0	0	15	15
147.0	0	8	8
148.0	0	15	15
149.0	0	13	13
150.0	0	8	8
151.0	0	10	10
152.0	0	12	12
153.0	0	8	8
154.0	0	16	16
155.0	0	11	11
156.0	0	9	9
157.0	0	9	9
158.0	0	11	11
159.0	0	12	12
160.0	0	16	16
161.0	0	8	8
162.0	0	9	9
163.0	0	11	11
164.0	0	9	9
165.0	0	7	7
166.0	0	13	13
167.0	0	10	10
168.0	0	9	9
169.0	0	9	9
170.0	0	2	2
171.0	0	6	6
172.0	0	12	12
173.0	0	11	11
174.0	0	7	7
175.0	0	11	11
176.0	0	6	6
177.0	0	7	7
178.0	0	9	9
179.0	0	5	5
180.0	0	8	8
181.0	0	3	3
182.0	0	6	6
183.0	0	2	2
184.0	0	8	8
185.0	0	2	2
186.0	0	5	5
187.0	0	9	9
188.0	0	8	8
189.0	0	8	8
190.0	0	2	2
191.0	0	7	7
192.0	0	10	10
193.0	0	7	7
194.0	0	5	5
195.0	0	5	5
196.0	0	6	6
197.0	0	11	11
198.0	0	5	5
199.0	0	10	10
200.0	0	5	5
201.0	0	2	2
202.0	0	5	5
203.0	0	8	8
204.0	0	5	5
205.0	0	9	9
206.0	0	4	4
207.0	0	3	3
208.0	0	3	3
209.0	0	7	7
210.0	0	7	7
211.0	0	6	6
212.0	0	4	4
213.0	0	6	6
214.0	0	3	3
215.0	0	3	3
216.0	0	10	10
217.0	0	6	6
218.0	0	1	1
219.0	0	6	6
220.0	0	6	6
221.0	0	4	4
222.0	0	7	7
223.0	0	7	7
224.0	0	4	4
225.0	0	3	3
226.0	0	5	5
227.0	0	7	7
228.0	0	1	1
229.0	0	1	1
230.0	0	5	5
231.0	0	3	3
232.0	0	3	3
233.0	0	3	3
234.0	0	2	2
235.0	0	4	4
236.0	0	5	5
238.0	0	3	3
239.0	0	1	1
240.0	0	8	8
241.0	0	1	1
242.0	0	8	8
243.0	0	1	1
244.0	0	3	3
245.0	0	3	3
246.0	0	1	1
247.0	0	4	4
248.0	0	4	4
249.0	0	6	6
250.0	0	6	6
251.0	0	1	1
252.0	0	1	1
253.0	0	3	3
254.0	0	4	4
255.0	0	1	1
256.0	0	2	2
257.0	0	4	4
258.0	0	5	5
259.0	0	2	2
260.0	0	1	1
261.0	0	2	2
262.0	0	3	3
263.0	0	1	1
264.0	0	5	5
265.0	0	1	1
266.0	0	3	3
267.0	0	6	6
268.0	0	2	2
269.0	0	2	2
270.0	0	3	3
271.0	0	1	1
272.0	0	3	3
274.0	0	1	1
275.0	0	5	5
277.0	0	2	2
278.0	0	2	2
279.0	0	3	3
280.0	0	4	4
282.0	0	3	3
283.0	0	1	1
284.0	0	1	1
285.0	0	2	2
286.0	0	3	3
287.0	0	4	4
288.0	0	3	3
290.0	0	2	2
291.0	0	2	2
292.0	0	1	1
293.0	0	1	1
295.0	0	3	3
296.0	0	2	2
298.0	0	1	1
300.0	0	2	2
301.0	0	2	2
302.0	0	1	1
304.0	0	3	3
305.0	0	3	3
306.0	0	1	1
307.0	0	4	4
308.0	0	2	2
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	2	2
314.0	0	2	2
315.0	0	1	1
317.0	0	2	2
318.0	0	1	1
319.0	0	2	2
320.0	0	3	3
321.0	0	4	4
322.0	0	1	1
323.0	0	1	1
324.0	0	3	3
325.0	0	2	2
326.0	0	2	2
331.0	0	1	1
332.0	0	2	2
333.0	0	3	3
334.0	0	2	2
335.0	0	1	1
336.0	0	3	3
337.0	0	3	3
339.0	0	2	2
340.0	0	1	1
342.0	0	3	3
343.0	0	1	1
345.0	0	2	2
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
352.0	0	3	3
353.0	0	1	1
355.0	0	1	1
356.0	0	1	1
359.0	0	2	2
360.0	0	3	3
364.0	0	2	2
365.0	0	1	1
366.0	0	3	3
368.0	0	1	1
369.0	0	1	1
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
373.0	0	1	1
374.0	0	2	2
379.0	0	1	1
380.0	0	1	1
381.0	0	1	1
382.0	0	2	2
386.0	0	1	1
391.0	0	1	1
392.0	0	2	2
393.0	0	1	1
394.0	0	2	2
397.0	0	1	1
398.0	0	1	1
401.0	0	1	1
402.0	0	2	2
404.0	0	1	1
405.0	0	1	1
407.0	0	1	1
408.0	0	2	2
409.0	0	2	2
410.0	0	2	2
412.0	0	1	1
415.0	0	1	1
416.0	0	2	2
417.0	0	1	1
419.0	0	1	1
420.0	0	1	1
423.0	0	1	1
426.0	0	2	2
429.0	0	1	1
430.0	0	2	2
432.0	0	1	1
433.0	0	1	1
437.0	0	1	1
438.0	0	1	1
439.0	0	1	1
440.0	0	3	3
442.0	0	1	1
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
447.0	0	1	1
448.0	0	1	1
455.0	0	1	1
457.0	0	1	1
461.0	0	1	1
462.0	0	1	1
463.0	0	1	1
468.0	0	1	1
471.0	0	1	1
478.0	0	4	4
479.0	0	1	1
481.0	0	1	1
486.0	0	1	1
488.0	0	1	1
489.0	0	1	1
492.0	0	1	1
495.0	0	1	1
500.0	0	2	2
502.0	0	1	1
504.0	0	1	1
506.0	0	1	1
507.0	0	2	2
511.0	0	1	1
512.0	0	2	2
514.0	0	1	1
517.0	0	2	2
518.0	0	2	2
520.0	0	1	1
523.0	0	1	1
524.0	0	1	1
527.0	0	1	1
528.0	0	1	1
531.0	0	1	1
533.0	0	1	1
536.0	0	1	1
537.0	0	1	1
541.0	0	1	1
546.0	0	1	1
547.0	0	1	1
551.0	0	1	1
560.0	0	1	1
565.0	0	1	1
566.0	0	1	1
570.0	0	1	1
575.0	0	1	1
581.0	0	1	1
595.0	0	1	1
601.0	0	1	1
604.0	0	1	1
612.0	0	1	1
625.0	0	1	1
632.0	0	1	1
635.0	0	1	1
645.0	0	1	1
652.0	0	1	1
653.0	0	1	1
663.0	0	1	1
666.0	0	1	1
670.0	0	1	1
672.0	0	1	1
684.0	0	1	1
693.0	0	1	1
695.0	0	1	1
700.0	0	1	1
702.0	0	1	1
720.0	0	1	1
725.0	0	1	1
727.0	0	1	1
731.0	0	1	1
732.0	0	2	2
747.0	0	1	1
750.0	0	1	1
759.0	0	1	1
760.0	0	1	1
768.0	0	1	1
783.0	0	1	1
791.0	0	1	1
792.0	0	1	1
798.0	0	1	1
803.0	0	1	1
806.0	0	1	1
829.0	0	1	1
833.0	0	1	1
848.0	0	1	1
867.0	0	1	1
874.0	0	1	1
889.0	0	1	1
890.0	0	1	1
902.0	0	2	2
912.0	0	2	2
918.0	0	1	1
923.0	0	1	1
933.0	0	1	1
934.0	0	1	1
940.0	0	1	1
946.0	0	1	1
947.0	0	1	1
950.0	0	1	1
953.0	0	1	1
954.0	0	2	2
955.0	0	1	1
957.0	0	1	1
975.0	0	1	1
995.0	0	1	1
1006.0	0	1	1
1007.0	0	1	1
1042.0	0	1	1
1068.0	0	1	1
1077.0	0	1	1
1108.0	0	1	1
1133.0	0	1	1
1175.0	0	1	1
1183.0	0	1	1
1203.0	0	1	1
1204.0	0	1	1
1244.0	0	1	1
1273.0	0	1	1
1328.0	0	1	1
1366.0	0	1	1
1374.0	0	1	1
1380.0	0	1	1
1859.0	0	1	1