## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/GRCh37-NP_Day19_supernatant_DMSO_A63_S6.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day19_supernatant_DMSO_A63_S6.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day19_supernatant_DMSO_A63_S6.samtools-coordinate.metrics.txt    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: Tue Aug 31 19:16:51 CEST 2021

## 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	157	20393369	0	0	52	2004513	5042	0.098293	97035053

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000222	17054196	0	17058312
2.0	1.810853	1156155	5036	1152753
3.0	2.467829	109789	3	109185
4.0	3.000275	26110	0	26028
5.0	3.431797	11910	0	11899
6.0	3.781524	7026	0	7014
7.0	4.06496	4567	0	4568
8.0	4.294672	3038	0	3033
9.0	4.480841	2275	0	2277
10.0	4.631722	1849	0	1850
11.0	4.754004	1315	0	1314
12.0	4.853107	1083	0	1082
13.0	4.933426	889	0	888
14.0	4.99852	762	0	761
15.0	5.051275	625	0	626
16.0	5.094031	524	0	523
17.0	5.128682	432	0	432
18.0	5.156766	396	0	396
19.0	5.179526	388	0	389
20.0	5.197972	340	0	340
21.0	5.212921	283	0	282
22.0	5.225037	290	0	290
23.0	5.234856	247	0	248
24.0	5.242814	184	0	184
25.0	5.249264	197	0	196
26.0	5.254491	173	0	173
27.0	5.258727	157	0	157
28.0	5.26216	182	0	183
29.0	5.264943	146	0	147
30.0	5.267198	147	0	145
31.0	5.269026	140	0	140
32.0	5.270507	133	0	134
33.0	5.271707	121	0	120
34.0	5.27268	98	0	98
35.0	5.273469	109	0	110
36.0	5.274108	105	0	105
37.0	5.274626	79	0	79
38.0	5.275045	79	0	78
39.0	5.275386	60	0	61
40.0	5.275661	72	0	72
41.0	5.275885	74	0	73
42.0	5.276066	76	0	77
43.0	5.276213	56	0	55
44.0	5.276332	69	0	69
45.0	5.276428	57	0	57
46.0	5.276506	51	0	52
47.0	5.276569	50	0	49
48.0	5.276621	50	0	50
49.0	5.276662	53	0	53
50.0	5.276696	48	0	48
51.0	5.276723	49	0	49
52.0	5.276745	40	0	41
53.0	5.276763	39	0	38
54.0	5.276778	41	0	41
55.0	5.27679	39	0	39
56.0	5.276799	44	0	44
57.0	5.276807	35	0	35
58.0	5.276813	36	0	36
59.0	5.276818	26	0	27
60.0	5.276822	30	0	30
61.0	5.276826	38	0	37
62.0	5.276829	29	0	29
63.0	5.276831	14	0	14
64.0	5.276833	27	0	27
65.0	5.276834	24	0	24
66.0	5.276835	25	0	25
67.0	5.276836	27	0	27
68.0	5.276837	26	0	26
69.0	5.276837	16	0	16
70.0	5.276838	23	0	23
71.0	5.276838	20	0	20
72.0	5.276839	10	0	10
73.0	5.276839	17	0	17
74.0	5.276839	18	0	18
75.0	5.276839	15	0	15
76.0	5.27684	21	0	21
77.0	5.27684	22	0	22
78.0	5.27684	10	0	10
79.0	5.27684	9	0	9
80.0	5.27684	16	0	16
81.0	5.27684	24	0	24
82.0	5.27684	9	0	9
83.0	5.27684	10	0	10
84.0	5.27684	7	0	7
85.0	5.27684	14	0	14
86.0	5.27684	12	0	12
87.0	5.27684	16	0	16
88.0	5.27684	10	0	10
89.0	5.27684	11	0	11
90.0	5.27684	9	0	9
91.0	5.27684	15	0	15
92.0	5.27684	8	0	8
93.0	5.27684	10	0	10
94.0	5.27684	10	0	10
95.0	5.27684	6	0	6
96.0	5.27684	6	0	6
97.0	5.27684	15	0	15
98.0	5.27684	4	0	4
99.0	5.27684	13	0	14
100.0	5.27684	9	0	9
101.0	0	13	0	12
102.0	0	9	0	9
103.0	0	10	0	11
104.0	0	4	0	3
105.0	0	9	0	9
106.0	0	6	0	6
107.0	0	8	0	8
108.0	0	3	0	3
109.0	0	6	0	6
110.0	0	7	0	7
111.0	0	8	0	8
112.0	0	8	0	8
113.0	0	4	0	4
114.0	0	6	0	6
115.0	0	8	0	8
116.0	0	7	0	7
117.0	0	7	0	7
118.0	0	7	0	7
119.0	0	3	0	3
120.0	0	5	0	5
121.0	0	11	0	11
122.0	0	4	0	4
123.0	0	5	0	5
124.0	0	8	0	8
125.0	0	4	0	4
126.0	0	7	0	7
127.0	0	5	0	6
128.0	0	4	0	3
129.0	0	4	0	4
130.0	0	6	0	6
131.0	0	4	0	4
132.0	0	3	0	3
133.0	0	7	0	7
134.0	0	6	0	6
135.0	0	2	0	2
136.0	0	4	0	4
137.0	0	7	0	7
138.0	0	4	0	4
139.0	0	7	0	7
140.0	0	6	0	6
141.0	0	3	0	3
142.0	0	4	0	4
143.0	0	2	0	2
144.0	0	3	0	4
145.0	0	6	0	5
146.0	0	4	0	5
147.0	0	3	0	2
148.0	0	5	0	5
149.0	0	3	0	3
150.0	0	2	0	2
151.0	0	5	0	5
152.0	0	2	0	2
153.0	0	2	0	2
154.0	0	2	0	2
155.0	0	4	0	4
156.0	0	3	0	4
157.0	0	4	0	3
158.0	0	1	0	1
159.0	0	2	0	2
160.0	0	1	0	1
161.0	0	3	0	3
162.0	0	2	0	2
163.0	0	4	0	4
164.0	0	4	0	4
165.0	0	4	0	4
166.0	0	2	0	2
167.0	0	3	0	3
168.0	0	3	0	3
169.0	0	4	0	4
170.0	0	3	0	3
171.0	0	4	0	4
172.0	0	5	0	5
173.0	0	5	0	5
174.0	0	2	0	2
175.0	0	3	0	3
176.0	0	4	0	4
177.0	0	5	0	5
178.0	0	5	0	5
179.0	0	4	0	4
181.0	0	4	0	4
182.0	0	2	0	2
183.0	0	2	0	2
184.0	0	5	0	5
185.0	0	1	0	1
186.0	0	2	0	2
188.0	0	6	0	6
189.0	0	2	0	2
190.0	0	1	0	1
192.0	0	3	0	3
193.0	0	3	0	3
194.0	0	1	0	1
195.0	0	3	0	3
196.0	0	2	0	2
197.0	0	1	0	1
198.0	0	1	0	1
200.0	0	2	0	2
201.0	0	1	0	1
202.0	0	4	0	4
203.0	0	2	0	2
204.0	0	2	0	2
205.0	0	2	0	2
206.0	0	1	0	2
207.0	0	3	0	2
209.0	0	3	0	3
210.0	0	1	0	1
211.0	0	1	0	1
212.0	0	2	0	2
213.0	0	1	0	1
214.0	0	1	0	1
215.0	0	3	0	3
216.0	0	1	0	1
217.0	0	2	0	2
219.0	0	2	0	2
220.0	0	1	0	1
221.0	0	2	0	2
224.0	0	2	0	2
225.0	0	3	0	3
226.0	0	3	0	3
227.0	0	1	0	1
228.0	0	1	0	1
230.0	0	4	0	4
231.0	0	2	0	2
232.0	0	1	0	1
233.0	0	1	0	1
234.0	0	1	0	1
238.0	0	2	0	2
239.0	0	1	0	1
240.0	0	1	0	1
242.0	0	1	0	1
243.0	0	2	0	2
244.0	0	1	0	1
247.0	0	3	0	3
248.0	0	2	0	2
250.0	0	1	0	1
252.0	0	3	0	3
253.0	0	1	0	1
254.0	0	1	0	1
255.0	0	1	0	1
259.0	0	1	0	1
261.0	0	1	0	1
262.0	0	1	0	1
263.0	0	1	0	1
268.0	0	1	0	1
269.0	0	1	0	1
274.0	0	2	0	2
277.0	0	1	0	1
278.0	0	1	0	1
279.0	0	2	0	2
281.0	0	1	0	1
282.0	0	1	0	1
285.0	0	1	0	1
287.0	0	1	0	1
288.0	0	1	0	1
292.0	0	0	0	1
293.0	0	3	0	2
294.0	0	1	0	1
295.0	0	1	0	1
296.0	0	1	0	1
297.0	0	1	0	1
298.0	0	2	0	2
299.0	0	2	0	2
300.0	0	1	0	1
303.0	0	1	0	1
305.0	0	1	0	1
311.0	0	2	0	2
312.0	0	1	0	1
315.0	0	1	0	1
316.0	0	1	0	1
317.0	0	1	0	1
318.0	0	1	0	1
319.0	0	1	0	1
320.0	0	1	0	1
321.0	0	2	0	2
324.0	0	1	0	1
336.0	0	1	0	1
341.0	0	1	0	1
344.0	0	1	0	1
351.0	0	1	0	1
353.0	0	1	0	1
358.0	0	1	0	1
363.0	0	2	0	2
365.0	0	1	0	1
369.0	0	1	0	1
370.0	0	1	0	1
379.0	0	1	0	1
383.0	0	1	0	1
400.0	0	1	0	1
419.0	0	2	0	2
427.0	0	2	0	2
428.0	0	1	0	1
434.0	0	1	0	1
435.0	0	0	0	1
436.0	0	1	0	0
440.0	0	1	0	1
446.0	0	1	0	1
447.0	0	2	0	2
453.0	0	1	0	1
459.0	0	1	0	1
462.0	0	1	0	1
472.0	0	1	0	1
473.0	0	1	0	1
474.0	0	1	0	1
479.0	0	1	0	1
480.0	0	1	0	1
483.0	0	1	0	1
487.0	0	1	0	1
490.0	0	0	0	1
491.0	0	1	0	0
502.0	0	1	0	2
503.0	0	1	0	0
505.0	0	1	0	1
533.0	0	1	0	1
565.0	0	1	0	1
572.0	0	1	0	1
579.0	0	1	0	2
580.0	0	1	0	0
589.0	0	1	0	1
595.0	0	1	0	1
616.0	0	1	0	1
626.0	0	1	0	1
637.0	0	1	0	1
641.0	0	1	0	1
649.0	0	1	0	1
659.0	0	1	0	1
701.0	0	1	0	1
721.0	0	1	0	1
736.0	0	1	0	1
738.0	0	1	0	1
758.0	0	1	0	1
773.0	0	1	0	1
810.0	0	1	0	1
941.0	0	1	0	1
974.0	0	1	0	1
1013.0	0	1	0	1
1036.0	0	1	0	1