## 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_100nM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_100nM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_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 19:20:57 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	1028886	40308274	0	1193510	754563	6270310	0	0.16284	115742807

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31093234	31093234
2.0	1.705917	2156655	2156655
3.0	2.204236	376904	376904
4.0	2.556008	144379	144379
5.0	2.80433	75952	75952
6.0	2.979625	45938	45938
7.0	3.103369	30220	30220
8.0	3.190722	21111	21111
9.0	3.252385	15386	15386
10.0	3.295915	11639	11639
11.0	3.326643	8897	8897
12.0	3.348335	7093	7093
13.0	3.363647	5792	5792
14.0	3.374457	4523	4523
15.0	3.382087	3979	3979
16.0	3.387474	3397	3397
17.0	3.391276	2930	2930
18.0	3.39396	2414	2414
19.0	3.395855	2108	2108
20.0	3.397193	1824	1824
21.0	3.398137	1629	1629
22.0	3.398803	1392	1392
23.0	3.399274	1304	1304
24.0	3.399606	1187	1187
25.0	3.399841	989	989
26.0	3.400006	937	937
27.0	3.400123	859	859
28.0	3.400205	746	746
29.0	3.400264	742	742
30.0	3.400305	672	672
31.0	3.400334	651	651
32.0	3.400354	555	555
33.0	3.400369	521	521
34.0	3.400379	478	478
35.0	3.400386	413	413
36.0	3.400391	440	440
37.0	3.400395	368	368
38.0	3.400397	351	351
39.0	3.400399	371	371
40.0	3.4004	326	326
41.0	3.400401	319	319
42.0	3.400402	269	269
43.0	3.400402	266	266
44.0	3.400403	257	257
45.0	3.400403	232	232
46.0	3.400403	216	216
47.0	3.400403	225	225
48.0	3.400403	202	202
49.0	3.400403	210	210
50.0	3.400403	172	172
51.0	3.400403	160	160
52.0	3.400403	173	173
53.0	3.400403	162	162
54.0	3.400403	149	149
55.0	3.400403	142	142
56.0	3.400403	147	147
57.0	3.400403	134	134
58.0	3.400403	147	147
59.0	3.400403	108	108
60.0	3.400403	121	121
61.0	3.400403	99	99
62.0	3.400403	96	96
63.0	3.400403	106	106
64.0	3.400403	85	85
65.0	3.400403	105	105
66.0	3.400403	99	99
67.0	3.400403	83	83
68.0	3.400403	88	88
69.0	3.400403	85	85
70.0	3.400403	83	83
71.0	3.400403	78	78
72.0	3.400403	86	86
73.0	3.400403	74	74
74.0	3.400403	71	71
75.0	3.400403	70	70
76.0	3.400403	64	64
77.0	3.400403	57	57
78.0	3.400403	65	65
79.0	3.400403	72	72
80.0	3.400403	61	61
81.0	3.400403	55	55
82.0	3.400403	57	57
83.0	3.400403	63	63
84.0	3.400403	61	61
85.0	3.400403	55	55
86.0	3.400403	47	47
87.0	3.400403	56	56
88.0	3.400403	39	39
89.0	3.400403	43	43
90.0	3.400403	47	47
91.0	3.400403	51	51
92.0	3.400403	34	34
93.0	3.400403	50	50
94.0	3.400403	52	52
95.0	3.400403	30	30
96.0	3.400403	40	40
97.0	3.400403	43	43
98.0	3.400403	47	47
99.0	3.400403	26	26
100.0	3.400403	37	37
101.0	0	34	34
102.0	0	37	37
103.0	0	29	29
104.0	0	32	32
105.0	0	28	28
106.0	0	32	32
107.0	0	27	27
108.0	0	25	25
109.0	0	30	30
110.0	0	17	17
111.0	0	25	25
112.0	0	29	29
113.0	0	31	31
114.0	0	21	21
115.0	0	26	26
116.0	0	23	23
117.0	0	21	21
118.0	0	23	23
119.0	0	24	24
120.0	0	18	18
121.0	0	19	19
122.0	0	12	12
123.0	0	26	26
124.0	0	21	21
125.0	0	24	24
126.0	0	23	23
127.0	0	17	17
128.0	0	17	17
129.0	0	19	19
130.0	0	20	20
131.0	0	23	23
132.0	0	20	20
133.0	0	18	18
134.0	0	20	20
135.0	0	13	13
136.0	0	12	12
137.0	0	15	15
138.0	0	19	19
139.0	0	15	15
140.0	0	15	15
141.0	0	19	19
142.0	0	5	5
143.0	0	12	12
144.0	0	17	17
145.0	0	7	7
146.0	0	10	10
147.0	0	10	10
148.0	0	18	18
149.0	0	13	13
150.0	0	10	10
151.0	0	16	16
152.0	0	9	9
153.0	0	18	18
154.0	0	13	13
155.0	0	13	13
156.0	0	15	15
157.0	0	14	14
158.0	0	7	7
159.0	0	15	15
160.0	0	13	13
161.0	0	14	14
162.0	0	16	16
163.0	0	16	16
164.0	0	14	14
165.0	0	11	11
166.0	0	17	17
167.0	0	8	8
168.0	0	10	10
169.0	0	9	9
170.0	0	12	12
171.0	0	14	14
172.0	0	5	5
173.0	0	16	16
174.0	0	13	13
175.0	0	9	9
176.0	0	11	11
177.0	0	6	6
178.0	0	7	7
179.0	0	9	9
180.0	0	8	8
181.0	0	9	9
182.0	0	4	4
183.0	0	7	7
184.0	0	1	1
185.0	0	8	8
186.0	0	1	1
187.0	0	8	8
188.0	0	3	3
189.0	0	12	12
190.0	0	6	6
191.0	0	6	6
192.0	0	10	10
193.0	0	8	8
194.0	0	5	5
195.0	0	7	7
196.0	0	8	8
197.0	0	6	6
198.0	0	6	6
199.0	0	5	5
200.0	0	11	11
201.0	0	15	15
202.0	0	8	8
203.0	0	10	10
204.0	0	7	7
205.0	0	5	5
206.0	0	6	6
207.0	0	7	7
208.0	0	2	2
209.0	0	9	9
210.0	0	8	8
211.0	0	4	4
212.0	0	6	6
213.0	0	7	7
214.0	0	3	3
215.0	0	4	4
216.0	0	11	11
217.0	0	3	3
218.0	0	1	1
219.0	0	6	6
220.0	0	5	5
221.0	0	6	6
222.0	0	3	3
223.0	0	3	3
224.0	0	6	6
225.0	0	6	6
226.0	0	2	2
227.0	0	4	4
228.0	0	5	5
229.0	0	6	6
230.0	0	4	4
231.0	0	7	7
232.0	0	6	6
233.0	0	4	4
234.0	0	8	8
235.0	0	6	6
236.0	0	8	8
237.0	0	4	4
238.0	0	2	2
239.0	0	5	5
240.0	0	3	3
241.0	0	3	3
242.0	0	3	3
243.0	0	2	2
244.0	0	5	5
245.0	0	4	4
246.0	0	3	3
247.0	0	6	6
248.0	0	3	3
249.0	0	3	3
250.0	0	2	2
251.0	0	2	2
252.0	0	2	2
253.0	0	6	6
254.0	0	8	8
255.0	0	2	2
256.0	0	3	3
257.0	0	4	4
258.0	0	4	4
259.0	0	7	7
260.0	0	1	1
261.0	0	1	1
262.0	0	4	4
263.0	0	7	7
264.0	0	2	2
265.0	0	4	4
266.0	0	3	3
267.0	0	6	6
268.0	0	5	5
269.0	0	4	4
270.0	0	4	4
271.0	0	3	3
272.0	0	3	3
273.0	0	5	5
274.0	0	1	1
276.0	0	2	2
277.0	0	5	5
278.0	0	4	4
279.0	0	1	1
280.0	0	4	4
281.0	0	3	3
282.0	0	7	7
283.0	0	3	3
284.0	0	4	4
285.0	0	4	4
287.0	0	3	3
288.0	0	2	2
289.0	0	2	2
290.0	0	1	1
291.0	0	4	4
292.0	0	4	4
293.0	0	1	1
294.0	0	3	3
295.0	0	3	3
296.0	0	2	2
297.0	0	3	3
298.0	0	3	3
299.0	0	3	3
300.0	0	3	3
301.0	0	3	3
302.0	0	3	3
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
308.0	0	1	1
309.0	0	2	2
310.0	0	1	1
312.0	0	1	1
313.0	0	1	1
314.0	0	3	3
315.0	0	2	2
316.0	0	2	2
317.0	0	3	3
318.0	0	1	1
319.0	0	2	2
320.0	0	1	1
321.0	0	2	2
323.0	0	4	4
326.0	0	2	2
327.0	0	2	2
328.0	0	2	2
329.0	0	1	1
330.0	0	1	1
332.0	0	1	1
333.0	0	2	2
334.0	0	2	2
335.0	0	1	1
336.0	0	2	2
337.0	0	1	1
338.0	0	2	2
339.0	0	1	1
340.0	0	4	4
341.0	0	1	1
342.0	0	3	3
343.0	0	2	2
344.0	0	2	2
345.0	0	1	1
346.0	0	2	2
347.0	0	1	1
348.0	0	2	2
349.0	0	3	3
350.0	0	2	2
351.0	0	4	4
352.0	0	2	2
353.0	0	2	2
354.0	0	1	1
355.0	0	3	3
356.0	0	3	3
357.0	0	2	2
359.0	0	2	2
360.0	0	2	2
361.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	2	2
365.0	0	1	1
366.0	0	3	3
367.0	0	2	2
370.0	0	4	4
371.0	0	3	3
372.0	0	1	1
373.0	0	2	2
377.0	0	1	1
378.0	0	1	1
381.0	0	1	1
382.0	0	1	1
383.0	0	1	1
384.0	0	2	2
385.0	0	1	1
386.0	0	4	4
387.0	0	2	2
389.0	0	3	3
390.0	0	4	4
392.0	0	2	2
393.0	0	2	2
398.0	0	2	2
402.0	0	3	3
403.0	0	1	1
404.0	0	1	1
405.0	0	1	1
406.0	0	2	2
407.0	0	1	1
413.0	0	1	1
414.0	0	1	1
416.0	0	2	2
417.0	0	1	1
418.0	0	1	1
420.0	0	1	1
422.0	0	1	1
423.0	0	1	1
425.0	0	3	3
428.0	0	2	2
429.0	0	1	1
432.0	0	1	1
435.0	0	2	2
436.0	0	1	1
441.0	0	2	2
446.0	0	2	2
447.0	0	1	1
450.0	0	1	1
454.0	0	1	1
455.0	0	2	2
457.0	0	1	1
461.0	0	1	1
462.0	0	1	1
464.0	0	1	1
465.0	0	4	4
467.0	0	2	2
469.0	0	1	1
470.0	0	2	2
472.0	0	1	1
476.0	0	2	2
478.0	0	2	2
480.0	0	1	1
481.0	0	1	1
482.0	0	2	2
485.0	0	1	1
486.0	0	3	3
488.0	0	1	1
489.0	0	1	1
493.0	0	1	1
497.0	0	1	1
499.0	0	1	1
501.0	0	2	2
502.0	0	1	1
504.0	0	1	1
505.0	0	1	1
506.0	0	1	1
507.0	0	1	1
508.0	0	1	1
512.0	0	1	1
514.0	0	1	1
515.0	0	1	1
517.0	0	1	1
518.0	0	1	1
521.0	0	2	2
526.0	0	1	1
528.0	0	1	1
533.0	0	1	1
536.0	0	1	1
537.0	0	1	1
543.0	0	1	1
544.0	0	1	1
551.0	0	2	2
552.0	0	1	1
553.0	0	1	1
555.0	0	2	2
556.0	0	1	1
558.0	0	1	1
559.0	0	1	1
561.0	0	1	1
563.0	0	1	1
569.0	0	2	2
570.0	0	1	1
574.0	0	1	1
576.0	0	1	1
577.0	0	1	1
578.0	0	1	1
579.0	0	2	2
580.0	0	1	1
584.0	0	1	1
589.0	0	1	1
592.0	0	1	1
594.0	0	1	1
598.0	0	1	1
604.0	0	2	2
605.0	0	1	1
608.0	0	1	1
624.0	0	1	1
630.0	0	1	1
632.0	0	1	1
637.0	0	1	1
641.0	0	1	1
647.0	0	1	1
649.0	0	1	1
659.0	0	1	1
661.0	0	1	1
666.0	0	1	1
668.0	0	1	1
672.0	0	1	1
682.0	0	1	1
687.0	0	1	1
695.0	0	2	2
700.0	0	1	1
701.0	0	3	3
704.0	0	1	1
708.0	0	1	1
713.0	0	1	1
715.0	0	1	1
717.0	0	1	1
719.0	0	1	1
725.0	0	1	1
733.0	0	1	1
738.0	0	1	1
742.0	0	1	1
749.0	0	1	1
750.0	0	1	1
780.0	0	1	1
788.0	0	1	1
790.0	0	1	1
807.0	0	1	1
808.0	0	1	1
809.0	0	1	1
815.0	0	1	1
817.0	0	1	1
820.0	0	1	1
829.0	0	1	1
849.0	0	1	1
859.0	0	1	1
863.0	0	1	1
870.0	0	1	1
873.0	0	1	1
874.0	0	1	1
876.0	0	1	1
877.0	0	1	1
889.0	0	1	1
894.0	0	1	1
896.0	0	1	1
911.0	0	1	1
930.0	0	1	1
937.0	0	1	1
952.0	0	1	1
993.0	0	1	1
1032.0	0	1	1
1052.0	0	1	1
1054.0	0	1	1
1081.0	0	1	1
1082.0	0	1	1
1092.0	0	1	1
1096.0	0	1	1
1145.0	0	1	1
1158.0	0	1	1
1164.0	0	1	1
1172.0	0	1	1
1204.0	0	1	1
1214.0	0	1	1
1218.0	0	1	1
1233.0	0	1	1
1252.0	0	1	1
1263.0	0	2	2
1265.0	0	1	1
1284.0	0	1	1
1305.0	0	1	1
1325.0	0	1	1
1335.0	0	1	1
1356.0	0	1	1
1406.0	0	1	1
1445.0	0	1	1
1448.0	0	1	1
2066.0	0	1	1