## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_RU_1uM.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_RU_1uM.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_RU_1uM.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: Wed Sep 14 14:30:41 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	2292	52988574	19686261	0	2127	10782994	0	0.203512	111857912

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	38581118	38581118
2.0	1.622686	2416592	2416592
3.0	2.010423	494696	494696
4.0	2.251862	213879	213879
5.0	2.402203	119655	119655
6.0	2.495817	76452	76452
7.0	2.55411	52947	52947
8.0	2.590408	38986	38986
9.0	2.61301	29382	29382
10.0	2.627084	22940	22940
11.0	2.635848	18509	18509
12.0	2.641305	15012	15012
13.0	2.644703	12396	12396
14.0	2.646819	10488	10488
15.0	2.648137	9125	9125
16.0	2.648957	7721	7721
17.0	2.649468	6709	6709
18.0	2.649786	5995	5995
19.0	2.649984	5062	5062
20.0	2.650107	4554	4554
21.0	2.650184	4172	4172
22.0	2.650232	3588	3588
23.0	2.650262	3276	3276
24.0	2.65028	3001	3001
25.0	2.650292	2676	2676
26.0	2.650299	2521	2521
27.0	2.650304	2276	2276
28.0	2.650306	2134	2134
29.0	2.650308	1899	1899
30.0	2.650309	1737	1737
31.0	2.65031	1563	1563
32.0	2.65031	1450	1450
33.0	2.650311	1402	1402
34.0	2.650311	1306	1306
35.0	2.650311	1190	1190
36.0	2.650311	1118	1118
37.0	2.650311	1074	1074
38.0	2.650311	991	991
39.0	2.650311	995	995
40.0	2.650311	895	895
41.0	2.650311	813	813
42.0	2.650311	809	809
43.0	2.650311	796	796
44.0	2.650311	759	759
45.0	2.650311	621	621
46.0	2.650311	666	666
47.0	2.650311	576	576
48.0	2.650311	538	538
49.0	2.650311	547	547
50.0	2.650311	535	535
51.0	2.650311	494	494
52.0	2.650311	496	496
53.0	2.650311	487	487
54.0	2.650311	443	443
55.0	2.650311	401	401
56.0	2.650311	400	400
57.0	2.650311	410	410
58.0	2.650311	378	378
59.0	2.650311	360	360
60.0	2.650311	361	361
61.0	2.650311	334	334
62.0	2.650311	301	301
63.0	2.650311	284	284
64.0	2.650311	268	268
65.0	2.650311	258	258
66.0	2.650311	244	244
67.0	2.650311	230	230
68.0	2.650311	243	243
69.0	2.650311	212	212
70.0	2.650311	241	241
71.0	2.650311	244	244
72.0	2.650311	205	205
73.0	2.650311	207	207
74.0	2.650311	206	206
75.0	2.650311	200	200
76.0	2.650311	206	206
77.0	2.650311	222	222
78.0	2.650311	162	162
79.0	2.650311	165	165
80.0	2.650311	159	159
81.0	2.650311	162	162
82.0	2.650311	172	172
83.0	2.650311	134	134
84.0	2.650311	144	144
85.0	2.650311	143	143
86.0	2.650311	156	156
87.0	2.650311	131	131
88.0	2.650311	146	146
89.0	2.650311	124	124
90.0	2.650311	148	148
91.0	2.650311	122	122
92.0	2.650311	119	119
93.0	2.650311	109	109
94.0	2.650311	106	106
95.0	2.650311	110	110
96.0	2.650311	107	107
97.0	2.650311	108	108
98.0	2.650311	97	97
99.0	2.650311	106	106
100.0	2.650311	86	86
101.0	0	96	96
102.0	0	79	79
103.0	0	65	65
104.0	0	76	76
105.0	0	95	95
106.0	0	90	90
107.0	0	72	72
108.0	0	89	89
109.0	0	65	65
110.0	0	59	59
111.0	0	79	79
112.0	0	73	73
113.0	0	74	74
114.0	0	78	78
115.0	0	76	76
116.0	0	79	79
117.0	0	55	55
118.0	0	72	72
119.0	0	55	55
120.0	0	59	59
121.0	0	52	52
122.0	0	47	47
123.0	0	53	53
124.0	0	64	64
125.0	0	64	64
126.0	0	54	54
127.0	0	56	56
128.0	0	44	44
129.0	0	43	43
130.0	0	60	60
131.0	0	50	50
132.0	0	53	53
133.0	0	36	36
134.0	0	39	39
135.0	0	46	46
136.0	0	39	39
137.0	0	68	68
138.0	0	38	38
139.0	0	46	46
140.0	0	46	46
141.0	0	46	46
142.0	0	47	47
143.0	0	35	35
144.0	0	34	34
145.0	0	37	37
146.0	0	47	47
147.0	0	16	16
148.0	0	36	36
149.0	0	24	24
150.0	0	36	36
151.0	0	30	30
152.0	0	42	42
153.0	0	26	26
154.0	0	25	25
155.0	0	25	25
156.0	0	40	40
157.0	0	30	30
158.0	0	24	24
159.0	0	37	37
160.0	0	26	26
161.0	0	26	26
162.0	0	26	26
163.0	0	14	14
164.0	0	23	23
165.0	0	23	23
166.0	0	29	29
167.0	0	20	20
168.0	0	27	27
169.0	0	25	25
170.0	0	31	31
171.0	0	26	26
172.0	0	31	31
173.0	0	22	22
174.0	0	24	24
175.0	0	32	32
176.0	0	24	24
177.0	0	23	23
178.0	0	18	18
179.0	0	22	22
180.0	0	22	22
181.0	0	16	16
182.0	0	27	27
183.0	0	19	19
184.0	0	22	22
185.0	0	25	25
186.0	0	16	16
187.0	0	13	13
188.0	0	14	14
189.0	0	13	13
190.0	0	18	18
191.0	0	19	19
192.0	0	18	18
193.0	0	18	18
194.0	0	15	15
195.0	0	17	17
196.0	0	10	10
197.0	0	15	15
198.0	0	15	15
199.0	0	16	16
200.0	0	16	16
201.0	0	18	18
202.0	0	20	20
203.0	0	15	15
204.0	0	14	14
205.0	0	18	18
206.0	0	7	7
207.0	0	22	22
208.0	0	14	14
209.0	0	12	12
210.0	0	17	17
211.0	0	10	10
212.0	0	7	7
213.0	0	13	13
214.0	0	10	10
215.0	0	18	18
216.0	0	10	10
217.0	0	14	14
218.0	0	13	13
219.0	0	23	23
220.0	0	21	21
221.0	0	6	6
222.0	0	15	15
223.0	0	13	13
224.0	0	10	10
225.0	0	16	16
226.0	0	12	12
227.0	0	13	13
228.0	0	8	8
229.0	0	10	10
230.0	0	13	13
231.0	0	8	8
232.0	0	11	11
233.0	0	13	13
234.0	0	13	13
235.0	0	7	7
236.0	0	11	11
237.0	0	11	11
238.0	0	10	10
239.0	0	9	9
240.0	0	6	6
241.0	0	9	9
242.0	0	8	8
243.0	0	12	12
244.0	0	12	12
245.0	0	13	13
246.0	0	15	15
247.0	0	6	6
248.0	0	11	11
249.0	0	14	14
250.0	0	12	12
251.0	0	10	10
252.0	0	9	9
253.0	0	11	11
254.0	0	6	6
255.0	0	9	9
256.0	0	13	13
257.0	0	11	11
258.0	0	5	5
259.0	0	9	9
260.0	0	6	6
261.0	0	13	13
262.0	0	11	11
263.0	0	5	5
264.0	0	7	7
265.0	0	11	11
266.0	0	5	5
267.0	0	11	11
268.0	0	11	11
269.0	0	6	6
270.0	0	7	7
271.0	0	9	9
272.0	0	5	5
273.0	0	8	8
274.0	0	12	12
275.0	0	3	3
276.0	0	8	8
277.0	0	11	11
278.0	0	4	4
279.0	0	9	9
280.0	0	11	11
281.0	0	6	6
282.0	0	8	8
283.0	0	7	7
284.0	0	8	8
285.0	0	6	6
286.0	0	8	8
287.0	0	11	11
288.0	0	8	8
289.0	0	4	4
290.0	0	12	12
291.0	0	6	6
292.0	0	3	3
293.0	0	10	10
294.0	0	9	9
295.0	0	6	6
296.0	0	4	4
297.0	0	5	5
298.0	0	9	9
299.0	0	7	7
300.0	0	5	5
301.0	0	10	10
302.0	0	13	13
303.0	0	5	5
304.0	0	4	4
305.0	0	4	4
306.0	0	4	4
307.0	0	3	3
308.0	0	5	5
309.0	0	7	7
310.0	0	6	6
311.0	0	5	5
312.0	0	5	5
313.0	0	4	4
314.0	0	4	4
315.0	0	5	5
316.0	0	7	7
317.0	0	7	7
318.0	0	1	1
319.0	0	4	4
320.0	0	6	6
321.0	0	8	8
322.0	0	6	6
323.0	0	3	3
324.0	0	5	5
325.0	0	9	9
326.0	0	6	6
327.0	0	10	10
328.0	0	6	6
329.0	0	8	8
330.0	0	5	5
331.0	0	3	3
332.0	0	8	8
333.0	0	10	10
334.0	0	3	3
335.0	0	2	2
336.0	0	3	3
337.0	0	5	5
338.0	0	3	3
339.0	0	2	2
340.0	0	4	4
341.0	0	4	4
342.0	0	5	5
343.0	0	2	2
344.0	0	2	2
345.0	0	3	3
346.0	0	6	6
347.0	0	4	4
348.0	0	8	8
349.0	0	3	3
350.0	0	4	4
351.0	0	4	4
352.0	0	2	2
353.0	0	4	4
354.0	0	7	7
355.0	0	4	4
356.0	0	6	6
357.0	0	1	1
358.0	0	6	6
359.0	0	4	4
360.0	0	2	2
361.0	0	2	2
362.0	0	3	3
363.0	0	5	5
364.0	0	3	3
365.0	0	3	3
366.0	0	3	3
367.0	0	3	3
368.0	0	2	2
369.0	0	6	6
370.0	0	4	4
371.0	0	2	2
373.0	0	2	2
374.0	0	4	4
375.0	0	5	5
376.0	0	2	2
377.0	0	2	2
378.0	0	9	9
379.0	0	5	5
380.0	0	4	4
381.0	0	4	4
382.0	0	3	3
383.0	0	3	3
384.0	0	4	4
385.0	0	3	3
386.0	0	2	2
387.0	0	1	1
388.0	0	1	1
389.0	0	6	6
390.0	0	3	3
391.0	0	4	4
392.0	0	1	1
393.0	0	5	5
394.0	0	1	1
395.0	0	3	3
396.0	0	5	5
397.0	0	1	1
398.0	0	2	2
399.0	0	2	2
400.0	0	2	2
401.0	0	2	2
402.0	0	5	5
403.0	0	1	1
404.0	0	2	2
405.0	0	1	1
406.0	0	2	2
407.0	0	2	2
408.0	0	5	5
409.0	0	2	2
410.0	0	2	2
411.0	0	1	1
412.0	0	5	5
413.0	0	5	5
414.0	0	2	2
415.0	0	1	1
416.0	0	3	3
417.0	0	2	2
419.0	0	2	2
420.0	0	4	4
421.0	0	4	4
422.0	0	3	3
423.0	0	1	1
424.0	0	4	4
425.0	0	4	4
426.0	0	5	5
427.0	0	3	3
428.0	0	1	1
429.0	0	4	4
430.0	0	2	2
431.0	0	3	3
432.0	0	1	1
433.0	0	2	2
434.0	0	3	3
435.0	0	4	4
436.0	0	2	2
437.0	0	2	2
438.0	0	5	5
440.0	0	2	2
441.0	0	1	1
442.0	0	7	7
444.0	0	6	6
445.0	0	1	1
446.0	0	2	2
447.0	0	3	3
448.0	0	3	3
449.0	0	3	3
451.0	0	1	1
452.0	0	5	5
453.0	0	1	1
454.0	0	2	2
455.0	0	2	2
456.0	0	2	2
457.0	0	1	1
458.0	0	1	1
459.0	0	1	1
460.0	0	2	2
461.0	0	4	4
462.0	0	2	2
463.0	0	5	5
464.0	0	2	2
465.0	0	2	2
466.0	0	4	4
468.0	0	2	2
469.0	0	1	1
470.0	0	2	2
471.0	0	2	2
472.0	0	3	3
473.0	0	4	4
474.0	0	3	3
475.0	0	1	1
476.0	0	2	2
477.0	0	2	2
478.0	0	2	2
479.0	0	5	5
480.0	0	3	3
482.0	0	2	2
483.0	0	2	2
484.0	0	3	3
487.0	0	1	1
488.0	0	1	1
489.0	0	1	1
491.0	0	3	3
492.0	0	4	4
493.0	0	2	2
494.0	0	1	1
495.0	0	3	3
498.0	0	2	2
499.0	0	2	2
500.0	0	1	1
502.0	0	2	2
503.0	0	2	2
504.0	0	1	1
505.0	0	2	2
507.0	0	1	1
508.0	0	2	2
511.0	0	5	5
512.0	0	2	2
513.0	0	4	4
514.0	0	1	1
515.0	0	2	2
516.0	0	2	2
519.0	0	1	1
520.0	0	3	3
521.0	0	2	2
522.0	0	1	1
523.0	0	1	1
525.0	0	3	3
526.0	0	2	2
527.0	0	1	1
528.0	0	1	1
530.0	0	1	1
531.0	0	2	2
533.0	0	1	1
535.0	0	1	1
537.0	0	1	1
538.0	0	3	3
541.0	0	2	2
543.0	0	4	4
545.0	0	2	2
546.0	0	6	6
547.0	0	3	3
549.0	0	1	1
551.0	0	1	1
553.0	0	2	2
554.0	0	1	1
556.0	0	2	2
557.0	0	1	1
558.0	0	3	3
560.0	0	2	2
561.0	0	3	3
562.0	0	2	2
565.0	0	4	4
566.0	0	1	1
567.0	0	2	2
568.0	0	1	1
570.0	0	2	2
571.0	0	1	1
572.0	0	3	3
574.0	0	1	1
575.0	0	2	2
576.0	0	1	1
577.0	0	2	2
579.0	0	1	1
582.0	0	1	1
584.0	0	1	1
586.0	0	1	1
588.0	0	2	2
589.0	0	2	2
590.0	0	1	1
592.0	0	1	1
593.0	0	2	2
594.0	0	2	2
595.0	0	1	1
596.0	0	2	2
597.0	0	1	1
598.0	0	1	1
599.0	0	1	1
600.0	0	1	1
601.0	0	1	1
602.0	0	2	2
604.0	0	1	1
605.0	0	1	1
606.0	0	1	1
608.0	0	1	1
611.0	0	2	2
612.0	0	2	2
613.0	0	1	1
615.0	0	3	3
616.0	0	1	1
618.0	0	1	1
619.0	0	1	1
622.0	0	2	2
623.0	0	1	1
624.0	0	2	2
625.0	0	1	1
626.0	0	1	1
628.0	0	1	1
629.0	0	2	2
630.0	0	2	2
637.0	0	2	2
640.0	0	1	1
642.0	0	2	2
643.0	0	1	1
644.0	0	2	2
645.0	0	1	1
646.0	0	2	2
653.0	0	4	4
656.0	0	1	1
657.0	0	2	2
658.0	0	1	1
661.0	0	1	1
663.0	0	1	1
667.0	0	1	1
668.0	0	1	1
670.0	0	1	1
671.0	0	2	2
672.0	0	1	1
674.0	0	1	1
677.0	0	1	1
678.0	0	2	2
679.0	0	3	3
680.0	0	2	2
681.0	0	2	2
682.0	0	1	1
686.0	0	1	1
688.0	0	2	2
690.0	0	1	1
691.0	0	2	2
692.0	0	1	1
693.0	0	2	2
696.0	0	2	2
697.0	0	3	3
701.0	0	1	1
703.0	0	2	2
706.0	0	2	2
707.0	0	1	1
708.0	0	2	2
709.0	0	1	1
710.0	0	1	1
714.0	0	2	2
715.0	0	1	1
716.0	0	1	1
720.0	0	2	2
721.0	0	1	1
723.0	0	1	1
728.0	0	1	1
729.0	0	1	1
731.0	0	1	1
733.0	0	1	1
734.0	0	3	3
736.0	0	1	1
737.0	0	1	1
742.0	0	1	1
744.0	0	1	1
745.0	0	1	1
746.0	0	1	1
750.0	0	1	1
751.0	0	2	2
757.0	0	1	1
762.0	0	1	1
765.0	0	1	1
766.0	0	1	1
772.0	0	1	1
776.0	0	1	1
777.0	0	3	3
782.0	0	1	1
785.0	0	1	1
787.0	0	1	1
788.0	0	1	1
793.0	0	1	1
799.0	0	1	1
801.0	0	1	1
803.0	0	1	1
807.0	0	2	2
814.0	0	1	1
815.0	0	1	1
816.0	0	1	1
820.0	0	2	2
825.0	0	1	1
826.0	0	1	1
830.0	0	2	2
832.0	0	1	1
833.0	0	1	1
834.0	0	1	1
835.0	0	1	1
838.0	0	1	1
841.0	0	1	1
843.0	0	1	1
844.0	0	2	2
845.0	0	1	1
847.0	0	1	1
849.0	0	1	1
851.0	0	1	1
852.0	0	1	1
854.0	0	1	1
857.0	0	1	1
860.0	0	1	1
866.0	0	1	1
873.0	0	1	1
874.0	0	1	1
878.0	0	1	1
881.0	0	1	1
885.0	0	1	1
887.0	0	1	1
888.0	0	1	1
889.0	0	2	2
890.0	0	1	1
898.0	0	1	1
899.0	0	1	1
903.0	0	2	2
911.0	0	1	1
914.0	0	1	1
915.0	0	1	1
928.0	0	1	1
930.0	0	1	1
931.0	0	1	1
936.0	0	2	2
937.0	0	2	2
939.0	0	1	1
940.0	0	1	1
942.0	0	1	1
951.0	0	1	1
966.0	0	1	1
975.0	0	1	1
976.0	0	1	1
980.0	0	2	2
993.0	0	1	1
999.0	0	1	1
1002.0	0	1	1
1022.0	0	1	1
1023.0	0	1	1
1029.0	0	1	1
1032.0	0	1	1
1037.0	0	1	1
1039.0	0	1	1
1045.0	0	1	1
1048.0	0	1	1
1049.0	0	1	1
1055.0	0	1	1
1060.0	0	1	1
1080.0	0	1	1
1092.0	0	1	1
1095.0	0	1	1
1106.0	0	1	1
1109.0	0	1	1
1112.0	0	1	1
1122.0	0	1	1
1125.0	0	1	1
1126.0	0	1	1
1131.0	0	1	1
1140.0	0	1	1
1151.0	0	1	1
1152.0	0	1	1
1156.0	0	1	1
1159.0	0	1	1
1165.0	0	1	1
1181.0	0	1	1
1184.0	0	1	1
1192.0	0	1	1
1202.0	0	1	1
1203.0	0	1	1
1204.0	0	1	1
1205.0	0	1	1
1220.0	0	1	1
1224.0	0	1	1
1241.0	0	2	2
1244.0	0	2	2
1247.0	0	1	1
1267.0	0	1	1
1286.0	0	1	1
1289.0	0	1	1
1311.0	0	1	1
1336.0	0	1	1
1344.0	0	1	1
1354.0	0	1	1
1367.0	0	1	1
1368.0	0	1	1
1370.0	0	1	1
1390.0	0	1	1
1406.0	0	1	1
1437.0	0	1	1
1442.0	0	1	1
1443.0	0	1	1
1461.0	0	1	1
1475.0	0	1	1
1491.0	0	1	1
1493.0	0	1	1
1497.0	0	1	1
1549.0	0	1	1
1553.0	0	1	1
1573.0	0	1	1
1606.0	0	1	1
1647.0	0	1	1
1734.0	0	1	1
1773.0	0	1	1
1836.0	0	1	1
1877.0	0	1	1
1893.0	0	1	1
1910.0	0	1	1
1959.0	0	1	1
1976.0	0	1	1
1981.0	0	1	1
2053.0	0	1	1
2056.0	0	1	1
2066.0	0	1	1
2083.0	0	1	1
2110.0	0	1	1
2120.0	0	1	1
2179.0	0	1	1
2194.0	0	1	1
2197.0	0	1	1
2239.0	0	1	1
2264.0	0	1	1
2365.0	0	1	1
2471.0	0	1	1
2542.0	0	1	1
2565.0	0	1	1
2604.0	0	1	1
2615.0	0	1	1
2630.0	0	1	1
2650.0	0	1	1
2680.0	0	1	1
2746.0	0	1	1
2756.0	0	1	1
2793.0	0	1	1
2796.0	0	1	1
2802.0	0	1	1
2812.0	0	1	1
2900.0	0	1	1
2959.0	0	1	1
3086.0	0	1	1
3315.0	0	1	1
3585.0	0	1	1
3607.0	0	1	1
3637.0	0	1	1
3775.0	0	1	1
4083.0	0	1	1
4322.0	0	1	1
6603.0	0	1	1
8229.0	0	1	1