## 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_1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-TA_1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-TA_1uM_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 18:39:11 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	1276844	51722208	0	1470652	984213	9563969	0	0.192054	122025605

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	37864766	37864766
2.0	1.654513	3048906	3048906
3.0	2.082901	573549	573549
4.0	2.363286	226257	226257
5.0	2.546802	122310	122310
6.0	2.666915	75757	75757
7.0	2.745531	50715	50715
8.0	2.796986	35329	35329
9.0	2.830664	26427	26427
10.0	2.852707	20346	20346
11.0	2.867134	15707	15707
12.0	2.876577	12463	12463
13.0	2.882758	10158	10158
14.0	2.886803	8435	8435
15.0	2.889451	7003	7003
16.0	2.891183	5796	5796
17.0	2.892318	4885	4885
18.0	2.89306	4346	4346
19.0	2.893546	3596	3596
20.0	2.893864	3305	3305
21.0	2.894072	2770	2770
22.0	2.894208	2539	2539
23.0	2.894297	2213	2213
24.0	2.894356	2030	2030
25.0	2.894394	1734	1734
26.0	2.894419	1604	1604
27.0	2.894435	1442	1442
28.0	2.894446	1309	1309
29.0	2.894453	1182	1182
30.0	2.894458	1125	1125
31.0	2.894461	1007	1007
32.0	2.894463	965	965
33.0	2.894464	859	859
34.0	2.894465	819	819
35.0	2.894465	766	766
36.0	2.894466	682	682
37.0	2.894466	631	631
38.0	2.894466	598	598
39.0	2.894466	571	571
40.0	2.894466	503	503
41.0	2.894466	505	505
42.0	2.894466	486	486
43.0	2.894466	429	429
44.0	2.894466	434	434
45.0	2.894466	371	371
46.0	2.894466	381	381
47.0	2.894466	332	332
48.0	2.894466	337	337
49.0	2.894466	309	309
50.0	2.894466	311	311
51.0	2.894466	293	293
52.0	2.894466	248	248
53.0	2.894466	242	242
54.0	2.894466	225	225
55.0	2.894466	229	229
56.0	2.894466	209	209
57.0	2.894466	223	223
58.0	2.894466	199	199
59.0	2.894466	195	195
60.0	2.894466	194	194
61.0	2.894466	165	165
62.0	2.894466	155	155
63.0	2.894466	174	174
64.0	2.894466	157	157
65.0	2.894466	144	144
66.0	2.894466	126	126
67.0	2.894466	144	144
68.0	2.894466	144	144
69.0	2.894466	109	109
70.0	2.894466	118	118
71.0	2.894466	124	124
72.0	2.894466	102	102
73.0	2.894466	114	114
74.0	2.894466	101	101
75.0	2.894466	107	107
76.0	2.894466	101	101
77.0	2.894466	95	95
78.0	2.894466	85	85
79.0	2.894466	82	82
80.0	2.894466	84	84
81.0	2.894466	93	93
82.0	2.894466	71	71
83.0	2.894466	92	92
84.0	2.894466	63	63
85.0	2.894466	70	70
86.0	2.894466	61	61
87.0	2.894466	85	85
88.0	2.894466	69	69
89.0	2.894466	64	64
90.0	2.894466	58	58
91.0	2.894466	58	58
92.0	2.894466	56	56
93.0	2.894466	72	72
94.0	2.894466	74	74
95.0	2.894466	52	52
96.0	2.894466	63	63
97.0	2.894466	50	50
98.0	2.894466	52	52
99.0	2.894466	46	46
100.0	2.894466	49	49
101.0	0	42	42
102.0	0	51	51
103.0	0	50	50
104.0	0	45	45
105.0	0	49	49
106.0	0	42	42
107.0	0	34	34
108.0	0	30	30
109.0	0	33	33
110.0	0	44	44
111.0	0	31	31
112.0	0	36	36
113.0	0	47	47
114.0	0	27	27
115.0	0	23	23
116.0	0	28	28
117.0	0	41	41
118.0	0	38	38
119.0	0	29	29
120.0	0	34	34
121.0	0	31	31
122.0	0	30	30
123.0	0	36	36
124.0	0	43	43
125.0	0	24	24
126.0	0	16	16
127.0	0	22	22
128.0	0	23	23
129.0	0	25	25
130.0	0	23	23
131.0	0	20	20
132.0	0	18	18
133.0	0	28	28
134.0	0	24	24
135.0	0	22	22
136.0	0	25	25
137.0	0	16	16
138.0	0	15	15
139.0	0	15	15
140.0	0	28	28
141.0	0	24	24
142.0	0	16	16
143.0	0	19	19
144.0	0	15	15
145.0	0	25	25
146.0	0	13	13
147.0	0	10	10
148.0	0	23	23
149.0	0	12	12
150.0	0	18	18
151.0	0	12	12
152.0	0	18	18
153.0	0	9	9
154.0	0	9	9
155.0	0	17	17
156.0	0	11	11
157.0	0	19	19
158.0	0	16	16
159.0	0	16	16
160.0	0	11	11
161.0	0	11	11
162.0	0	16	16
163.0	0	12	12
164.0	0	11	11
165.0	0	22	22
166.0	0	18	18
167.0	0	21	21
168.0	0	12	12
169.0	0	11	11
170.0	0	13	13
171.0	0	8	8
172.0	0	11	11
173.0	0	13	13
174.0	0	10	10
175.0	0	6	6
176.0	0	12	12
177.0	0	14	14
178.0	0	12	12
179.0	0	13	13
180.0	0	11	11
181.0	0	15	15
182.0	0	8	8
183.0	0	14	14
184.0	0	10	10
185.0	0	16	16
186.0	0	11	11
187.0	0	10	10
188.0	0	8	8
189.0	0	9	9
190.0	0	7	7
191.0	0	5	5
192.0	0	7	7
193.0	0	13	13
194.0	0	10	10
195.0	0	7	7
196.0	0	9	9
197.0	0	11	11
198.0	0	5	5
199.0	0	8	8
200.0	0	6	6
201.0	0	10	10
202.0	0	6	6
203.0	0	6	6
204.0	0	8	8
205.0	0	16	16
206.0	0	5	5
207.0	0	12	12
208.0	0	7	7
209.0	0	7	7
210.0	0	8	8
211.0	0	12	12
212.0	0	2	2
213.0	0	7	7
214.0	0	6	6
215.0	0	9	9
216.0	0	7	7
217.0	0	5	5
218.0	0	10	10
219.0	0	6	6
220.0	0	5	5
221.0	0	6	6
222.0	0	6	6
223.0	0	6	6
224.0	0	4	4
225.0	0	7	7
226.0	0	9	9
227.0	0	8	8
228.0	0	4	4
229.0	0	6	6
230.0	0	10	10
231.0	0	7	7
232.0	0	7	7
233.0	0	10	10
234.0	0	5	5
235.0	0	6	6
236.0	0	5	5
237.0	0	6	6
238.0	0	5	5
239.0	0	2	2
240.0	0	12	12
241.0	0	4	4
242.0	0	5	5
243.0	0	4	4
244.0	0	4	4
245.0	0	12	12
246.0	0	8	8
247.0	0	8	8
248.0	0	1	1
249.0	0	3	3
250.0	0	6	6
251.0	0	4	4
252.0	0	5	5
253.0	0	6	6
254.0	0	5	5
255.0	0	6	6
256.0	0	6	6
257.0	0	4	4
258.0	0	3	3
259.0	0	6	6
260.0	0	4	4
261.0	0	6	6
262.0	0	4	4
263.0	0	3	3
264.0	0	4	4
265.0	0	2	2
266.0	0	2	2
267.0	0	6	6
268.0	0	6	6
269.0	0	2	2
270.0	0	3	3
271.0	0	4	4
272.0	0	1	1
273.0	0	2	2
274.0	0	5	5
275.0	0	4	4
276.0	0	1	1
277.0	0	7	7
278.0	0	4	4
279.0	0	5	5
280.0	0	1	1
281.0	0	3	3
282.0	0	2	2
283.0	0	6	6
284.0	0	5	5
285.0	0	4	4
287.0	0	3	3
288.0	0	2	2
289.0	0	1	1
290.0	0	3	3
291.0	0	3	3
292.0	0	2	2
293.0	0	2	2
294.0	0	3	3
295.0	0	6	6
296.0	0	2	2
297.0	0	2	2
298.0	0	5	5
299.0	0	2	2
300.0	0	5	5
301.0	0	5	5
302.0	0	2	2
303.0	0	1	1
306.0	0	3	3
307.0	0	4	4
308.0	0	2	2
309.0	0	1	1
310.0	0	6	6
311.0	0	1	1
312.0	0	2	2
314.0	0	3	3
315.0	0	2	2
316.0	0	3	3
317.0	0	3	3
318.0	0	1	1
319.0	0	1	1
320.0	0	4	4
321.0	0	5	5
322.0	0	4	4
323.0	0	3	3
324.0	0	1	1
325.0	0	1	1
326.0	0	2	2
327.0	0	3	3
328.0	0	1	1
329.0	0	2	2
330.0	0	3	3
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	4	4
337.0	0	3	3
338.0	0	3	3
340.0	0	2	2
341.0	0	1	1
342.0	0	3	3
343.0	0	3	3
344.0	0	4	4
345.0	0	4	4
346.0	0	2	2
347.0	0	1	1
348.0	0	2	2
349.0	0	4	4
350.0	0	2	2
351.0	0	1	1
352.0	0	2	2
353.0	0	1	1
355.0	0	3	3
356.0	0	2	2
359.0	0	3	3
360.0	0	2	2
361.0	0	1	1
363.0	0	4	4
364.0	0	3	3
366.0	0	1	1
367.0	0	2	2
368.0	0	3	3
370.0	0	2	2
371.0	0	3	3
372.0	0	2	2
373.0	0	1	1
374.0	0	1	1
375.0	0	2	2
376.0	0	2	2
377.0	0	2	2
378.0	0	2	2
379.0	0	3	3
381.0	0	1	1
383.0	0	1	1
384.0	0	1	1
385.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	2	2
389.0	0	1	1
390.0	0	1	1
393.0	0	2	2
395.0	0	3	3
396.0	0	1	1
397.0	0	1	1
398.0	0	2	2
401.0	0	2	2
402.0	0	1	1
403.0	0	2	2
404.0	0	2	2
407.0	0	3	3
408.0	0	1	1
410.0	0	3	3
411.0	0	1	1
414.0	0	1	1
416.0	0	2	2
418.0	0	1	1
420.0	0	1	1
421.0	0	1	1
423.0	0	3	3
425.0	0	1	1
426.0	0	2	2
429.0	0	2	2
431.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	2	2
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
438.0	0	4	4
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
446.0	0	1	1
449.0	0	1	1
453.0	0	1	1
455.0	0	1	1
456.0	0	2	2
458.0	0	2	2
459.0	0	2	2
460.0	0	1	1
462.0	0	1	1
463.0	0	1	1
465.0	0	1	1
468.0	0	1	1
474.0	0	1	1
476.0	0	1	1
477.0	0	2	2
478.0	0	1	1
481.0	0	1	1
483.0	0	1	1
484.0	0	2	2
486.0	0	1	1
488.0	0	1	1
491.0	0	1	1
492.0	0	1	1
493.0	0	1	1
496.0	0	1	1
498.0	0	1	1
501.0	0	2	2
503.0	0	1	1
504.0	0	1	1
505.0	0	1	1
506.0	0	1	1
508.0	0	1	1
511.0	0	1	1
512.0	0	1	1
514.0	0	2	2
516.0	0	2	2
523.0	0	1	1
524.0	0	4	4
531.0	0	1	1
534.0	0	2	2
540.0	0	1	1
542.0	0	2	2
545.0	0	2	2
546.0	0	1	1
549.0	0	2	2
551.0	0	3	3
552.0	0	1	1
553.0	0	1	1
554.0	0	3	3
555.0	0	1	1
557.0	0	1	1
558.0	0	1	1
561.0	0	1	1
562.0	0	1	1
564.0	0	1	1
566.0	0	1	1
569.0	0	1	1
573.0	0	1	1
576.0	0	1	1
581.0	0	1	1
586.0	0	1	1
587.0	0	1	1
589.0	0	2	2
595.0	0	1	1
598.0	0	2	2
600.0	0	2	2
602.0	0	1	1
605.0	0	1	1
607.0	0	2	2
608.0	0	1	1
615.0	0	1	1
619.0	0	1	1
620.0	0	1	1
623.0	0	1	1
624.0	0	1	1
625.0	0	1	1
629.0	0	1	1
631.0	0	1	1
633.0	0	1	1
637.0	0	1	1
640.0	0	1	1
643.0	0	1	1
646.0	0	1	1
649.0	0	3	3
659.0	0	1	1
661.0	0	1	1
665.0	0	1	1
666.0	0	1	1
670.0	0	1	1
671.0	0	2	2
677.0	0	1	1
679.0	0	3	3
682.0	0	1	1
684.0	0	1	1
693.0	0	1	1
695.0	0	2	2
699.0	0	1	1
700.0	0	1	1
704.0	0	2	2
709.0	0	1	1
711.0	0	1	1
719.0	0	1	1
725.0	0	1	1
729.0	0	1	1
730.0	0	1	1
735.0	0	1	1
740.0	0	1	1
758.0	0	1	1
770.0	0	1	1
771.0	0	1	1
772.0	0	1	1
775.0	0	1	1
778.0	0	1	1
782.0	0	1	1
785.0	0	1	1
793.0	0	1	1
800.0	0	1	1
805.0	0	2	2
818.0	0	1	1
828.0	0	1	1
833.0	0	1	1
848.0	0	1	1
851.0	0	1	1
853.0	0	1	1
867.0	0	2	2
868.0	0	1	1
870.0	0	1	1
874.0	0	1	1
877.0	0	1	1
881.0	0	1	1
884.0	0	1	1
888.0	0	1	1
899.0	0	2	2
902.0	0	1	1
903.0	0	1	1
905.0	0	2	2
911.0	0	1	1
912.0	0	1	1
917.0	0	1	1
929.0	0	1	1
930.0	0	1	1
932.0	0	1	1
933.0	0	1	1
936.0	0	1	1
939.0	0	1	1
941.0	0	1	1
942.0	0	1	1
949.0	0	1	1
957.0	0	1	1
966.0	0	1	1
970.0	0	1	1
983.0	0	1	1
986.0	0	1	1
987.0	0	1	1
994.0	0	1	1
1049.0	0	1	1
1050.0	0	1	1
1094.0	0	1	1
1108.0	0	1	1
1130.0	0	1	1
1166.0	0	1	1
1177.0	0	1	1
1224.0	0	1	1
1241.0	0	1	1
1267.0	0	1	1
1346.0	0	1	1
1382.0	0	1	1
1523.0	0	1	1
1593.0	0	1	1
1655.0	0	1	1
1790.0	0	1	1
1795.0	0	1	1
1825.0	0	1	1
1872.0	0	1	1
1926.0	0	1	1
1940.0	0	1	1
2003.0	0	1	1
2133.0	0	1	1
2646.0	0	1	1