## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/hg38-NP_Day19_supernatant_DMSO_A63_S6.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day19_supernatant_DMSO_A63_S6.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-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: Mon Aug 30 14:01:49 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	156	20324608	0	0	51	1973773	5026	0.097113	97971333

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000223	17024933	0	17029040
2.0	1.813054	1151171	5020	1147773
3.0	2.473601	107995	3	107395
4.0	3.010394	25183	0	25101
5.0	3.44662	11343	0	11334
6.0	3.801119	6632	0	6619
7.0	4.089202	4305	0	4306
8.0	4.323313	2846	0	2841
9.0	4.513563	2150	0	2152
10.0	4.66817	1751	0	1752
11.0	4.793812	1240	0	1238
12.0	4.895914	1036	0	1036
13.0	4.978888	834	0	833
14.0	5.046316	721	0	720
15.0	5.101112	584	0	585
16.0	5.145642	492	0	491
17.0	5.181829	412	0	412
18.0	5.211236	378	0	378
19.0	5.235134	368	0	369
20.0	5.254555	323	0	323
21.0	5.270337	265	0	264
22.0	5.283163	281	0	281
23.0	5.293585	236	0	237
24.0	5.302055	180	0	180
25.0	5.308938	191	0	190
26.0	5.314532	164	0	164
27.0	5.319077	144	0	144
28.0	5.322771	175	0	176
29.0	5.325773	141	0	142
30.0	5.328213	140	0	138
31.0	5.330195	136	0	136
32.0	5.331806	128	0	129
33.0	5.333115	119	0	118
34.0	5.334179	94	0	94
35.0	5.335044	104	0	105
36.0	5.335747	101	0	101
37.0	5.336318	77	0	77
38.0	5.336782	80	0	79
39.0	5.337159	58	0	59
40.0	5.337465	71	0	71
41.0	5.337714	74	0	73
42.0	5.337916	74	0	75
43.0	5.338081	56	0	55
44.0	5.338215	68	0	68
45.0	5.338323	52	0	52
46.0	5.338411	50	0	51
47.0	5.338483	48	0	47
48.0	5.338541	48	0	48
49.0	5.338589	52	0	52
50.0	5.338627	48	0	48
51.0	5.338659	48	0	48
52.0	5.338684	40	0	41
53.0	5.338705	39	0	38
54.0	5.338721	40	0	40
55.0	5.338735	39	0	39
56.0	5.338746	43	0	43
57.0	5.338755	34	0	34
58.0	5.338763	35	0	35
59.0	5.338768	26	0	27
60.0	5.338773	29	0	29
61.0	5.338777	37	0	36
62.0	5.33878	29	0	29
63.0	5.338783	14	0	14
64.0	5.338785	27	0	27
65.0	5.338787	23	0	23
66.0	5.338788	25	0	25
67.0	5.338789	27	0	27
68.0	5.33879	25	0	25
69.0	5.338791	16	0	16
70.0	5.338792	22	0	22
71.0	5.338792	19	0	19
72.0	5.338793	10	0	10
73.0	5.338793	17	0	17
74.0	5.338793	18	0	18
75.0	5.338793	15	0	15
76.0	5.338794	21	0	21
77.0	5.338794	21	0	21
78.0	5.338794	10	0	10
79.0	5.338794	9	0	9
80.0	5.338794	15	0	15
81.0	5.338794	24	0	24
82.0	5.338794	8	0	8
83.0	5.338794	10	0	10
84.0	5.338794	7	0	7
85.0	5.338794	14	0	14
86.0	5.338794	11	0	11
87.0	5.338794	16	0	16
88.0	5.338794	10	0	10
89.0	5.338794	10	0	10
90.0	5.338794	9	0	9
91.0	5.338794	14	0	14
92.0	5.338794	7	0	7
93.0	5.338794	9	0	9
94.0	5.338794	9	0	9
95.0	5.338794	6	0	6
96.0	5.338794	6	0	6
97.0	5.338794	15	0	15
98.0	5.338794	4	0	4
99.0	5.338794	13	0	14
100.0	5.338794	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	7	0	7
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	10	0	10
122.0	0	5	0	5
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	3	0	3
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	4	0	4
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	2	0	2
193.0	0	4	0	4
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