## 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_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-TA_100nM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-TA_100nM_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 18:03:15 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	1213594	47245429	0	1389796	923796	9251919	0	0.202996	104306320

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	33841357	33841357
2.0	1.635751	2997426	2997426
3.0	2.03993	549750	549750
4.0	2.296887	208766	208766
5.0	2.460247	110132	110132
6.0	2.564104	67406	67406
7.0	2.630131	45039	45039
8.0	2.672107	31822	31822
9.0	2.698794	23046	23046
10.0	2.71576	17620	17620
11.0	2.726546	13711	13711
12.0	2.733403	10805	10805
13.0	2.737763	8854	8854
14.0	2.740535	7214	7214
15.0	2.742297	5889	5889
16.0	2.743417	4990	4990
17.0	2.744129	4297	4297
18.0	2.744582	3681	3681
19.0	2.74487	3243	3243
20.0	2.745053	2753	2753
21.0	2.745169	2402	2402
22.0	2.745243	2233	2233
23.0	2.74529	1906	1906
24.0	2.74532	1741	1741
25.0	2.745339	1523	1523
26.0	2.745351	1337	1337
27.0	2.745359	1280	1280
28.0	2.745364	1173	1173
29.0	2.745367	1089	1089
30.0	2.745369	971	971
31.0	2.74537	887	887
32.0	2.745371	891	891
33.0	2.745371	778	778
34.0	2.745371	675	675
35.0	2.745372	675	675
36.0	2.745372	598	598
37.0	2.745372	564	564
38.0	2.745372	511	511
39.0	2.745372	525	525
40.0	2.745372	502	502
41.0	2.745372	429	429
42.0	2.745372	419	419
43.0	2.745372	420	420
44.0	2.745372	385	385
45.0	2.745372	351	351
46.0	2.745372	370	370
47.0	2.745372	342	342
48.0	2.745372	338	338
49.0	2.745372	286	286
50.0	2.745372	318	318
51.0	2.745372	251	251
52.0	2.745372	226	226
53.0	2.745372	231	231
54.0	2.745372	230	230
55.0	2.745372	214	214
56.0	2.745372	199	199
57.0	2.745372	197	197
58.0	2.745372	192	192
59.0	2.745372	187	187
60.0	2.745372	192	192
61.0	2.745372	197	197
62.0	2.745372	179	179
63.0	2.745372	167	167
64.0	2.745372	165	165
65.0	2.745372	154	154
66.0	2.745372	163	163
67.0	2.745372	121	121
68.0	2.745372	146	146
69.0	2.745372	110	110
70.0	2.745372	124	124
71.0	2.745372	131	131
72.0	2.745372	123	123
73.0	2.745372	106	106
74.0	2.745372	108	108
75.0	2.745372	111	111
76.0	2.745372	111	111
77.0	2.745372	105	105
78.0	2.745372	100	100
79.0	2.745372	81	81
80.0	2.745372	88	88
81.0	2.745372	89	89
82.0	2.745372	90	90
83.0	2.745372	81	81
84.0	2.745372	76	76
85.0	2.745372	77	77
86.0	2.745372	47	47
87.0	2.745372	82	82
88.0	2.745372	68	68
89.0	2.745372	70	70
90.0	2.745372	79	79
91.0	2.745372	77	77
92.0	2.745372	49	49
93.0	2.745372	52	52
94.0	2.745372	56	56
95.0	2.745372	57	57
96.0	2.745372	49	49
97.0	2.745372	64	64
98.0	2.745372	52	52
99.0	2.745372	45	45
100.0	2.745372	51	51
101.0	0	54	54
102.0	0	51	51
103.0	0	60	60
104.0	0	49	49
105.0	0	46	46
106.0	0	48	48
107.0	0	50	50
108.0	0	40	40
109.0	0	40	40
110.0	0	35	35
111.0	0	44	44
112.0	0	41	41
113.0	0	39	39
114.0	0	38	38
115.0	0	47	47
116.0	0	38	38
117.0	0	45	45
118.0	0	41	41
119.0	0	30	30
120.0	0	38	38
121.0	0	41	41
122.0	0	33	33
123.0	0	32	32
124.0	0	35	35
125.0	0	38	38
126.0	0	27	27
127.0	0	32	32
128.0	0	24	24
129.0	0	34	34
130.0	0	48	48
131.0	0	22	22
132.0	0	26	26
133.0	0	29	29
134.0	0	26	26
135.0	0	26	26
136.0	0	22	22
137.0	0	29	29
138.0	0	27	27
139.0	0	14	14
140.0	0	20	20
141.0	0	18	18
142.0	0	18	18
143.0	0	26	26
144.0	0	10	10
145.0	0	21	21
146.0	0	24	24
147.0	0	25	25
148.0	0	27	27
149.0	0	24	24
150.0	0	19	19
151.0	0	11	11
152.0	0	17	17
153.0	0	24	24
154.0	0	20	20
155.0	0	18	18
156.0	0	20	20
157.0	0	16	16
158.0	0	12	12
159.0	0	22	22
160.0	0	23	23
161.0	0	15	15
162.0	0	14	14
163.0	0	14	14
164.0	0	21	21
165.0	0	16	16
166.0	0	16	16
167.0	0	20	20
168.0	0	17	17
169.0	0	12	12
170.0	0	17	17
171.0	0	19	19
172.0	0	7	7
173.0	0	16	16
174.0	0	6	6
175.0	0	14	14
176.0	0	12	12
177.0	0	19	19
178.0	0	6	6
179.0	0	9	9
180.0	0	9	9
181.0	0	13	13
182.0	0	19	19
183.0	0	11	11
184.0	0	15	15
185.0	0	17	17
186.0	0	11	11
187.0	0	13	13
188.0	0	12	12
189.0	0	11	11
190.0	0	5	5
191.0	0	13	13
192.0	0	10	10
193.0	0	7	7
194.0	0	16	16
195.0	0	9	9
196.0	0	11	11
197.0	0	10	10
198.0	0	13	13
199.0	0	14	14
200.0	0	8	8
201.0	0	14	14
202.0	0	12	12
203.0	0	8	8
204.0	0	13	13
205.0	0	19	19
206.0	0	10	10
207.0	0	7	7
208.0	0	13	13
209.0	0	12	12
210.0	0	8	8
211.0	0	9	9
212.0	0	8	8
213.0	0	10	10
214.0	0	8	8
215.0	0	7	7
216.0	0	10	10
217.0	0	8	8
218.0	0	10	10
219.0	0	9	9
220.0	0	7	7
221.0	0	10	10
222.0	0	7	7
223.0	0	6	6
224.0	0	6	6
225.0	0	14	14
226.0	0	8	8
227.0	0	9	9
228.0	0	6	6
229.0	0	9	9
230.0	0	3	3
231.0	0	6	6
232.0	0	13	13
233.0	0	1	1
234.0	0	10	10
235.0	0	8	8
236.0	0	13	13
237.0	0	9	9
238.0	0	8	8
239.0	0	4	4
240.0	0	9	9
241.0	0	8	8
242.0	0	11	11
243.0	0	8	8
244.0	0	9	9
245.0	0	5	5
246.0	0	8	8
247.0	0	6	6
248.0	0	9	9
249.0	0	7	7
250.0	0	8	8
251.0	0	8	8
252.0	0	3	3
253.0	0	8	8
254.0	0	6	6
255.0	0	8	8
256.0	0	5	5
257.0	0	5	5
258.0	0	8	8
259.0	0	5	5
260.0	0	9	9
261.0	0	4	4
262.0	0	14	14
263.0	0	8	8
264.0	0	6	6
265.0	0	6	6
266.0	0	6	6
267.0	0	2	2
268.0	0	9	9
269.0	0	5	5
270.0	0	8	8
271.0	0	4	4
272.0	0	7	7
273.0	0	2	2
274.0	0	8	8
275.0	0	5	5
276.0	0	9	9
277.0	0	2	2
278.0	0	9	9
280.0	0	5	5
281.0	0	6	6
282.0	0	5	5
283.0	0	3	3
284.0	0	4	4
285.0	0	2	2
286.0	0	6	6
287.0	0	5	5
288.0	0	1	1
289.0	0	5	5
290.0	0	3	3
291.0	0	4	4
292.0	0	4	4
293.0	0	2	2
294.0	0	10	10
295.0	0	6	6
296.0	0	2	2
297.0	0	7	7
298.0	0	4	4
299.0	0	2	2
300.0	0	4	4
301.0	0	6	6
302.0	0	2	2
303.0	0	1	1
304.0	0	1	1
305.0	0	7	7
306.0	0	5	5
307.0	0	3	3
308.0	0	3	3
309.0	0	1	1
311.0	0	4	4
312.0	0	3	3
313.0	0	5	5
314.0	0	1	1
315.0	0	2	2
316.0	0	3	3
317.0	0	4	4
318.0	0	5	5
319.0	0	3	3
320.0	0	7	7
321.0	0	5	5
322.0	0	5	5
323.0	0	2	2
324.0	0	5	5
325.0	0	3	3
326.0	0	7	7
327.0	0	1	1
328.0	0	5	5
330.0	0	2	2
331.0	0	1	1
332.0	0	3	3
333.0	0	1	1
334.0	0	3	3
335.0	0	3	3
336.0	0	3	3
337.0	0	3	3
338.0	0	3	3
339.0	0	4	4
340.0	0	2	2
341.0	0	7	7
342.0	0	3	3
343.0	0	1	1
346.0	0	9	9
347.0	0	3	3
348.0	0	3	3
349.0	0	3	3
350.0	0	3	3
351.0	0	3	3
352.0	0	6	6
353.0	0	9	9
354.0	0	3	3
355.0	0	3	3
356.0	0	2	2
357.0	0	2	2
358.0	0	3	3
359.0	0	3	3
360.0	0	5	5
361.0	0	5	5
362.0	0	1	1
363.0	0	4	4
364.0	0	2	2
365.0	0	2	2
367.0	0	2	2
368.0	0	1	1
369.0	0	4	4
370.0	0	1	1
371.0	0	3	3
372.0	0	1	1
373.0	0	3	3
374.0	0	3	3
375.0	0	2	2
376.0	0	5	5
377.0	0	2	2
378.0	0	2	2
379.0	0	1	1
381.0	0	2	2
382.0	0	1	1
383.0	0	3	3
384.0	0	1	1
385.0	0	2	2
386.0	0	6	6
387.0	0	1	1
388.0	0	1	1
389.0	0	1	1
390.0	0	4	4
391.0	0	3	3
392.0	0	1	1
393.0	0	1	1
394.0	0	2	2
395.0	0	1	1
396.0	0	2	2
398.0	0	2	2
399.0	0	1	1
401.0	0	3	3
402.0	0	2	2
404.0	0	2	2
406.0	0	2	2
407.0	0	3	3
408.0	0	2	2
409.0	0	5	5
411.0	0	2	2
412.0	0	4	4
413.0	0	1	1
414.0	0	1	1
415.0	0	1	1
416.0	0	1	1
417.0	0	3	3
418.0	0	3	3
419.0	0	1	1
420.0	0	3	3
421.0	0	1	1
422.0	0	3	3
423.0	0	2	2
424.0	0	3	3
425.0	0	1	1
426.0	0	2	2
428.0	0	1	1
429.0	0	2	2
430.0	0	2	2
432.0	0	5	5
433.0	0	2	2
436.0	0	1	1
437.0	0	1	1
438.0	0	1	1
439.0	0	1	1
440.0	0	5	5
442.0	0	1	1
444.0	0	2	2
445.0	0	1	1
446.0	0	2	2
447.0	0	1	1
448.0	0	1	1
450.0	0	1	1
452.0	0	2	2
453.0	0	1	1
455.0	0	2	2
457.0	0	1	1
458.0	0	3	3
459.0	0	1	1
460.0	0	3	3
461.0	0	1	1
462.0	0	1	1
464.0	0	1	1
467.0	0	2	2
471.0	0	2	2
472.0	0	1	1
474.0	0	2	2
476.0	0	2	2
478.0	0	2	2
480.0	0	1	1
482.0	0	2	2
485.0	0	1	1
487.0	0	1	1
488.0	0	1	1
489.0	0	2	2
491.0	0	3	3
492.0	0	3	3
493.0	0	1	1
495.0	0	1	1
496.0	0	1	1
498.0	0	1	1
499.0	0	1	1
501.0	0	1	1
502.0	0	1	1
503.0	0	1	1
504.0	0	2	2
505.0	0	1	1
506.0	0	2	2
507.0	0	1	1
510.0	0	2	2
513.0	0	1	1
514.0	0	1	1
515.0	0	1	1
516.0	0	1	1
518.0	0	1	1
519.0	0	2	2
520.0	0	2	2
521.0	0	2	2
522.0	0	3	3
523.0	0	2	2
526.0	0	1	1
527.0	0	3	3
528.0	0	1	1
529.0	0	3	3
532.0	0	1	1
533.0	0	1	1
538.0	0	3	3
539.0	0	2	2
540.0	0	1	1
543.0	0	1	1
544.0	0	1	1
546.0	0	2	2
549.0	0	2	2
551.0	0	2	2
552.0	0	2	2
553.0	0	2	2
554.0	0	2	2
555.0	0	1	1
557.0	0	1	1
558.0	0	2	2
559.0	0	1	1
560.0	0	1	1
561.0	0	2	2
562.0	0	1	1
564.0	0	1	1
565.0	0	1	1
566.0	0	2	2
567.0	0	1	1
568.0	0	1	1
569.0	0	1	1
570.0	0	1	1
572.0	0	2	2
576.0	0	1	1
583.0	0	1	1
584.0	0	2	2
587.0	0	4	4
589.0	0	1	1
590.0	0	2	2
591.0	0	1	1
594.0	0	1	1
595.0	0	1	1
597.0	0	1	1
600.0	0	3	3
605.0	0	1	1
610.0	0	2	2
614.0	0	1	1
615.0	0	1	1
619.0	0	1	1
621.0	0	3	3
623.0	0	1	1
626.0	0	1	1
628.0	0	1	1
631.0	0	1	1
632.0	0	2	2
633.0	0	1	1
634.0	0	1	1
639.0	0	1	1
640.0	0	1	1
643.0	0	1	1
650.0	0	1	1
656.0	0	1	1
657.0	0	1	1
660.0	0	1	1
666.0	0	1	1
668.0	0	1	1
670.0	0	1	1
680.0	0	1	1
684.0	0	1	1
685.0	0	1	1
689.0	0	1	1
692.0	0	1	1
695.0	0	1	1
696.0	0	1	1
697.0	0	1	1
704.0	0	1	1
708.0	0	1	1
711.0	0	2	2
712.0	0	2	2
718.0	0	1	1
725.0	0	1	1
732.0	0	1	1
734.0	0	1	1
735.0	0	1	1
736.0	0	1	1
742.0	0	1	1
743.0	0	1	1
753.0	0	2	2
756.0	0	1	1
763.0	0	1	1
766.0	0	1	1
767.0	0	1	1
771.0	0	1	1
775.0	0	1	1
779.0	0	1	1
784.0	0	1	1
790.0	0	1	1
792.0	0	2	2
793.0	0	1	1
798.0	0	1	1
799.0	0	2	2
803.0	0	1	1
808.0	0	2	2
810.0	0	1	1
815.0	0	1	1
818.0	0	1	1
824.0	0	2	2
830.0	0	1	1
837.0	0	1	1
843.0	0	1	1
852.0	0	1	1
854.0	0	1	1
855.0	0	1	1
861.0	0	2	2
865.0	0	1	1
866.0	0	1	1
867.0	0	1	1
876.0	0	1	1
879.0	0	1	1
887.0	0	1	1
890.0	0	3	3
898.0	0	1	1
900.0	0	1	1
901.0	0	1	1
904.0	0	2	2
905.0	0	1	1
914.0	0	2	2
921.0	0	1	1
923.0	0	1	1
929.0	0	1	1
930.0	0	1	1
932.0	0	1	1
933.0	0	1	1
940.0	0	1	1
944.0	0	1	1
946.0	0	1	1
955.0	0	1	1
966.0	0	2	2
968.0	0	1	1
970.0	0	1	1
971.0	0	1	1
975.0	0	1	1
983.0	0	1	1
984.0	0	1	1
991.0	0	1	1
996.0	0	1	1
999.0	0	1	1
1014.0	0	1	1
1029.0	0	1	1
1032.0	0	1	1
1057.0	0	1	1
1064.0	0	1	1
1070.0	0	1	1
1075.0	0	1	1
1076.0	0	1	1
1086.0	0	1	1
1088.0	0	1	1
1093.0	0	1	1
1109.0	0	1	1
1110.0	0	1	1
1118.0	0	1	1
1133.0	0	1	1
1154.0	0	1	1
1155.0	0	1	1
1160.0	0	1	1
1167.0	0	1	1
1176.0	0	1	1
1184.0	0	1	1
1194.0	0	1	1
1203.0	0	1	1
1214.0	0	1	1
1228.0	0	1	1
1247.0	0	1	1
1263.0	0	1	1
1271.0	0	1	1
1272.0	0	1	1
1274.0	0	1	1
1279.0	0	2	2
1282.0	0	1	1
1286.0	0	1	1
1296.0	0	1	1
1299.0	0	1	1
1313.0	0	1	1
1325.0	0	1	1
1332.0	0	1	1
1338.0	0	1	1
1353.0	0	1	1
1360.0	0	1	1
1377.0	0	1	1
1394.0	0	1	1
1412.0	0	1	1
1493.0	0	1	1
1545.0	0	1	1
1561.0	0	1	1
1584.0	0	1	1
1590.0	0	1	1
1598.0	0	1	1
1611.0	0	1	1
1631.0	0	1	1
1640.0	0	1	1
1701.0	0	1	1
1727.0	0	1	1
1735.0	0	1	1
1739.0	0	1	1
1823.0	0	1	1
1844.0	0	1	1
1873.0	0	1	1
1935.0	0	1	1
1958.0	0	2	2
1987.0	0	1	1
2053.0	0	1	1
2123.0	0	1	1
2149.0	0	1	1
2196.0	0	1	1
2816.0	0	1	1
2979.0	0	1	1
4033.0	0	1	1