## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[gonad.sorted.bam] OUTPUT=gonad.markdup.sorted.bam METRICS_FILE=gonad.markdup.sorted.MarkDuplicates.metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true TMP_DIR=[tmp] VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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 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 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: Fri Mar 25 10:19:19 GMT 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	97788	41017159	6564515	0	76410	38816184	0	0.946144	2200975

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	279315	279315
2.0	1	98779	98779
3.0	1	65939	65939
4.0	1	53282	53282
5.0	1	47810	47810
6.0	1	45561	45561
7.0	1	46474	46474
8.0	1	48377	48377
9.0	1	51026	51026
10.0	1	54420	54420
11.0	1	58000	58000
12.0	1	60626	60626
13.0	1	62671	62671
14.0	1	63450	63450
15.0	1	63923	63923
16.0	1	63234	63234
17.0	1	60612	60612
18.0	1	58183	58183
19.0	1	56169	56169
20.0	1	53947	53947
21.0	1	52648	52648
22.0	1	50608	50608
23.0	1	48520	48520
24.0	1	46885	46885
25.0	1	45058	45058
26.0	1	43056	43056
27.0	1	40653	40653
28.0	1	38364	38364
29.0	1	35821	35821
30.0	1	33057	33057
31.0	1	30628	30628
32.0	1	27904	27904
33.0	1	24977	24977
34.0	1	22320	22320
35.0	1	20118	20118
36.0	1	17690	17690
37.0	1	15737	15737
38.0	1	13891	13891
39.0	1	12719	12719
40.0	1	11481	11481
41.0	1	10208	10208
42.0	1	9387	9387
43.0	1	8586	8586
44.0	1	8024	8024
45.0	1	7705	7705
46.0	1	7244	7244
47.0	1	6894	6894
48.0	1	6710	6710
49.0	1	6327	6327
50.0	1	6215	6215
51.0	1	5881	5881
52.0	1	5591	5591
53.0	1	5481	5481
54.0	1	5172	5172
55.0	1	5027	5027
56.0	1	4667	4667
57.0	1	4627	4627
58.0	1	4320	4320
59.0	1	4089	4089
60.0	1	3666	3666
61.0	1	3633	3633
62.0	1	3280	3280
63.0	1	3070	3070
64.0	1	2772	2772
65.0	1	2600	2600
66.0	1	2324	2324
67.0	1	2117	2117
68.0	1	1943	1943
69.0	1	1810	1810
70.0	1	1479	1479
71.0	1	1493	1493
72.0	1	1328	1328
73.0	1	1165	1165
74.0	1	1055	1055
75.0	1	967	967
76.0	1	858	858
77.0	1	782	782
78.0	1	735	735
79.0	1	653	653
80.0	1	700	700
81.0	1	561	561
82.0	1	552	552
83.0	1	527	527
84.0	1	446	446
85.0	1	396	396
86.0	1	397	397
87.0	1	408	408
88.0	1	369	369
89.0	1	314	314
90.0	1	309	309
91.0	1	348	348
92.0	1	303	303
93.0	1	302	302
94.0	1	276	276
95.0	1	280	280
96.0	1	251	251
97.0	1	239	239
98.0	1	270	270
99.0	1	208	208
100.0	1	215	215
101.0	0	194	194
102.0	0	208	208
103.0	0	227	227
104.0	0	200	200
105.0	0	190	190
106.0	0	181	181
107.0	0	173	173
108.0	0	175	175
109.0	0	173	173
110.0	0	154	154
111.0	0	167	167
112.0	0	143	143
113.0	0	145	145
114.0	0	131	131
115.0	0	161	161
116.0	0	118	118
117.0	0	108	108
118.0	0	145	145
119.0	0	117	117
120.0	0	102	102
121.0	0	106	106
122.0	0	101	101
123.0	0	99	99
124.0	0	110	110
125.0	0	103	103
126.0	0	103	103
127.0	0	84	84
128.0	0	86	86
129.0	0	89	89
130.0	0	105	105
131.0	0	87	87
132.0	0	103	103
133.0	0	95	95
134.0	0	83	83
135.0	0	78	78
136.0	0	76	76
137.0	0	68	68
138.0	0	86	86
139.0	0	70	70
140.0	0	76	76
141.0	0	75	75
142.0	0	76	76
143.0	0	74	74
144.0	0	78	78
145.0	0	69	69
146.0	0	60	60
147.0	0	71	71
148.0	0	51	51
149.0	0	68	68
150.0	0	69	69
151.0	0	63	63
152.0	0	59	59
153.0	0	57	57
154.0	0	57	57
155.0	0	49	49
156.0	0	47	47
157.0	0	49	49
158.0	0	50	50
159.0	0	47	47
160.0	0	51	51
161.0	0	49	49
162.0	0	48	48
163.0	0	59	59
164.0	0	34	34
165.0	0	49	49
166.0	0	43	43
167.0	0	53	53
168.0	0	34	34
169.0	0	43	43
170.0	0	43	43
171.0	0	43	43
172.0	0	43	43
173.0	0	39	39
174.0	0	30	30
175.0	0	39	39
176.0	0	35	35
177.0	0	53	53
178.0	0	24	24
179.0	0	26	26
180.0	0	23	23
181.0	0	26	26
182.0	0	37	37
183.0	0	36	36
184.0	0	30	30
185.0	0	33	33
186.0	0	23	23
187.0	0	33	33
188.0	0	27	27
189.0	0	29	29
190.0	0	30	30
191.0	0	25	25
192.0	0	22	22
193.0	0	32	32
194.0	0	23	23
195.0	0	23	23
196.0	0	17	17
197.0	0	31	31
198.0	0	25	25
199.0	0	26	26
200.0	0	24	24
201.0	0	24	24
202.0	0	22	22
203.0	0	24	24
204.0	0	33	33
205.0	0	23	23
206.0	0	12	12
207.0	0	35	35
208.0	0	18	18
209.0	0	14	14
210.0	0	8	8
211.0	0	17	17
212.0	0	19	19
213.0	0	12	12
214.0	0	23	23
215.0	0	18	18
216.0	0	13	13
217.0	0	13	13
218.0	0	20	20
219.0	0	22	22
220.0	0	11	11
221.0	0	15	15
222.0	0	16	16
223.0	0	7	7
224.0	0	17	17
225.0	0	16	16
226.0	0	13	13
227.0	0	16	16
228.0	0	12	12
229.0	0	11	11
230.0	0	11	11
231.0	0	10	10
232.0	0	6	6
233.0	0	15	15
234.0	0	10	10
235.0	0	11	11
236.0	0	9	9
237.0	0	15	15
238.0	0	20	20
239.0	0	11	11
240.0	0	15	15
241.0	0	12	12
242.0	0	11	11
243.0	0	11	11
244.0	0	8	8
245.0	0	23	23
246.0	0	8	8
247.0	0	11	11
248.0	0	11	11
249.0	0	9	9
250.0	0	9	9
251.0	0	13	13
252.0	0	7	7
253.0	0	11	11
254.0	0	6	6
255.0	0	12	12
256.0	0	14	14
257.0	0	12	12
258.0	0	6	6
259.0	0	12	12
260.0	0	6	6
261.0	0	10	10
262.0	0	8	8
263.0	0	10	10
264.0	0	6	6
265.0	0	7	7
266.0	0	14	14
267.0	0	9	9
268.0	0	8	8
269.0	0	8	8
270.0	0	6	6
271.0	0	4	4
272.0	0	5	5
273.0	0	12	12
274.0	0	9	9
275.0	0	8	8
276.0	0	9	9
277.0	0	5	5
278.0	0	6	6
279.0	0	6	6
280.0	0	11	11
281.0	0	4	4
282.0	0	2	2
283.0	0	8	8
284.0	0	11	11
285.0	0	11	11
286.0	0	11	11
287.0	0	5	5
288.0	0	6	6
289.0	0	9	9
290.0	0	9	9
291.0	0	7	7
292.0	0	6	6
293.0	0	9	9
294.0	0	7	7
295.0	0	9	9
296.0	0	7	7
297.0	0	5	5
298.0	0	4	4
299.0	0	13	13
300.0	0	7	7
301.0	0	10	10
302.0	0	8	8
303.0	0	6	6
304.0	0	9	9
305.0	0	1	1
306.0	0	5	5
307.0	0	11	11
308.0	0	3	3
309.0	0	5	5
310.0	0	4	4
311.0	0	9	9
312.0	0	7	7
313.0	0	10	10
314.0	0	4	4
315.0	0	1	1
316.0	0	4	4
317.0	0	4	4
318.0	0	5	5
319.0	0	5	5
320.0	0	10	10
321.0	0	2	2
322.0	0	5	5
323.0	0	4	4
324.0	0	3	3
325.0	0	4	4
326.0	0	6	6
327.0	0	4	4
328.0	0	5	5
329.0	0	2	2
330.0	0	5	5
331.0	0	6	6
332.0	0	2	2
333.0	0	5	5
334.0	0	2	2
335.0	0	4	4
336.0	0	4	4
337.0	0	4	4
338.0	0	3	3
339.0	0	1	1
340.0	0	3	3
341.0	0	3	3
342.0	0	4	4
343.0	0	5	5
344.0	0	1	1
345.0	0	2	2
346.0	0	1	1
347.0	0	3	3
348.0	0	2	2
349.0	0	2	2
350.0	0	1	1
352.0	0	8	8
353.0	0	3	3
354.0	0	2	2
355.0	0	2	2
356.0	0	4	4
357.0	0	1	1
358.0	0	2	2
359.0	0	2	2
360.0	0	5	5
361.0	0	4	4
362.0	0	7	7
363.0	0	4	4
364.0	0	3	3
365.0	0	2	2
367.0	0	2	2
368.0	0	6	6
369.0	0	5	5
370.0	0	3	3
371.0	0	1	1
373.0	0	3	3
374.0	0	5	5
375.0	0	2	2
376.0	0	2	2
377.0	0	4	4
378.0	0	3	3
379.0	0	5	5
380.0	0	3	3
381.0	0	2	2
382.0	0	2	2
383.0	0	2	2
384.0	0	3	3
385.0	0	3	3
386.0	0	2	2
387.0	0	1	1
388.0	0	2	2
389.0	0	3	3
390.0	0	2	2
391.0	0	1	1
392.0	0	2	2
393.0	0	1	1
394.0	0	2	2
395.0	0	3	3
396.0	0	2	2
397.0	0	3	3
399.0	0	2	2
400.0	0	4	4
401.0	0	3	3
402.0	0	3	3
403.0	0	3	3
404.0	0	2	2
405.0	0	1	1
406.0	0	3	3
407.0	0	2	2
409.0	0	3	3
410.0	0	1	1
412.0	0	2	2
413.0	0	1	1
415.0	0	2	2
416.0	0	1	1
417.0	0	2	2
418.0	0	2	2
419.0	0	4	4
420.0	0	5	5
421.0	0	2	2
422.0	0	2	2
423.0	0	2	2
426.0	0	1	1
427.0	0	1	1
428.0	0	2	2
429.0	0	5	5
430.0	0	2	2
432.0	0	2	2
433.0	0	7	7
434.0	0	2	2
436.0	0	1	1
437.0	0	3	3
438.0	0	4	4
439.0	0	2	2
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	6	6
444.0	0	2	2
445.0	0	3	3
447.0	0	2	2
448.0	0	1	1
449.0	0	1	1
450.0	0	2	2
451.0	0	1	1
452.0	0	2	2
453.0	0	1	1
454.0	0	2	2
455.0	0	2	2
456.0	0	1	1
457.0	0	3	3
458.0	0	6	6
459.0	0	4	4
460.0	0	1	1
461.0	0	2	2
462.0	0	1	1
464.0	0	2	2
465.0	0	1	1
466.0	0	1	1
467.0	0	1	1
468.0	0	1	1
469.0	0	3	3
470.0	0	2	2
472.0	0	1	1
473.0	0	5	5
474.0	0	1	1
476.0	0	1	1
477.0	0	2	2
478.0	0	2	2
480.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	2	2
485.0	0	2	2
486.0	0	2	2
487.0	0	1	1
488.0	0	1	1
492.0	0	1	1
493.0	0	2	2
496.0	0	1	1
498.0	0	3	3
499.0	0	2	2
501.0	0	1	1
503.0	0	1	1
506.0	0	3	3
508.0	0	2	2
509.0	0	2	2
511.0	0	1	1
512.0	0	2	2
516.0	0	2	2
518.0	0	3	3
519.0	0	1	1
520.0	0	3	3
521.0	0	3	3
522.0	0	1	1
523.0	0	2	2
525.0	0	4	4
526.0	0	1	1
527.0	0	1	1
529.0	0	2	2
533.0	0	1	1
536.0	0	1	1
538.0	0	1	1
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
543.0	0	2	2
545.0	0	3	3
546.0	0	1	1
547.0	0	1	1
549.0	0	1	1
552.0	0	1	1
553.0	0	1	1
555.0	0	1	1
557.0	0	2	2
562.0	0	4	4
564.0	0	1	1
565.0	0	1	1
566.0	0	2	2
571.0	0	1	1
572.0	0	2	2
573.0	0	1	1
574.0	0	1	1
576.0	0	1	1
577.0	0	3	3
578.0	0	1	1
580.0	0	2	2
581.0	0	1	1
583.0	0	2	2
585.0	0	2	2
586.0	0	1	1
590.0	0	1	1
591.0	0	2	2
592.0	0	2	2
599.0	0	1	1
600.0	0	1	1
602.0	0	1	1
603.0	0	1	1
604.0	0	3	3
605.0	0	2	2
606.0	0	1	1
609.0	0	1	1
610.0	0	1	1
611.0	0	1	1
614.0	0	1	1
616.0	0	1	1
617.0	0	1	1
619.0	0	2	2
620.0	0	1	1
625.0	0	2	2
629.0	0	1	1
636.0	0	1	1
639.0	0	1	1
641.0	0	1	1
643.0	0	2	2
650.0	0	2	2
651.0	0	1	1
658.0	0	1	1
661.0	0	1	1
663.0	0	1	1
668.0	0	1	1
671.0	0	2	2
678.0	0	1	1
681.0	0	1	1
682.0	0	1	1
684.0	0	1	1
685.0	0	1	1
686.0	0	1	1
690.0	0	1	1
691.0	0	1	1
694.0	0	1	1
696.0	0	1	1
705.0	0	1	1
721.0	0	2	2
732.0	0	1	1
737.0	0	1	1
738.0	0	1	1
740.0	0	2	2
741.0	0	1	1
742.0	0	1	1
745.0	0	1	1
752.0	0	1	1
762.0	0	1	1
770.0	0	1	1
775.0	0	1	1
777.0	0	1	1
785.0	0	1	1
788.0	0	1	1
790.0	0	1	1
797.0	0	1	1
813.0	0	1	1
818.0	0	1	1
819.0	0	1	1
826.0	0	1	1
827.0	0	1	1
829.0	0	1	1
832.0	0	1	1
836.0	0	1	1
837.0	0	1	1
839.0	0	1	1
841.0	0	1	1
844.0	0	1	1
895.0	0	1	1
916.0	0	1	1
931.0	0	1	1
940.0	0	1	1
948.0	0	1	1
969.0	0	1	1
976.0	0	1	1
983.0	0	1	1
989.0	0	1	1
993.0	0	1	1
1007.0	0	1	1
1037.0	0	1	1
1048.0	0	1	1
1052.0	0	1	1
1082.0	0	1	1
1094.0	0	1	1
1140.0	0	1	1
1159.0	0	1	1
1161.0	0	1	1
1172.0	0	1	1
1174.0	0	1	1
1183.0	0	1	1
1208.0	0	1	1
1214.0	0	1	1
1219.0	0	1	1
1272.0	0	1	1
1329.0	0	1	1
1347.0	0	1	1
1367.0	0	1	1
1410.0	0	1	1
1636.0	0	1	1
1684.0	0	1	1
1741.0	0	1	1
1939.0	0	1	1
2002.0	0	1	1
2212.0	0	1	1
3441.0	0	1	1
4024.0	0	1	1
4474.0	0	1	1
132823.0	0	1	1